Disrupting FC receptor engagement on macrophages enhances efficacy of anti-SIRPalpha antibody therapy

ABSTRACT

Anti-SIRPα antibodies, including multi-specific anti-SIRPα antibodies, are provided, as are related compositions and methods. The antibodies of the disclosure bind to SIRPα and can block the interaction of CD47 on one cell with SIRPα on a phagocytic cell. The subject anti-SIRPα antibodies find use in various therapeutic methods. Embodiments of the disclosure include isolated antibodies and derivatives and fragments thereof, pharmaceutical formulations comprising one or more of the anti-SIRPα antibodies; and cell lines that produce the antibodies. Also provided are amino acid sequences of exemplary anti-SIRPα antibodies.

CROSS REFERENCE

This application claims benefit and is a Continuation of applicationSer. No. 15/660,510, filed Jul. 26, 2017, which claims benefit of U.S.Provisional Patent Application No. 62/370,422, filed Aug. 3, 2016, whichapplication is incorporated herein by reference in its entirety.

BACKGROUND OF THE INVENTION

Turnover of cells begins with the induction of an apoptotic program orother cellular changes that mark them for removal, and the subsequentrecognition of markers by phagocytes, including macrophages, dendriticcells, and the like. This process requires a specific and selectiveremoval of unwanted cells. Unlike healthy cells, the unwanted/aged/dyingcells display markers or ligands called “eat-me” signals, i.e. “alteredself”, which can in turn be recognized by receptors on the phagocytes.Healthy cells may display “don't eat-me” signals that actively inhibitphagocytosis; these signals are either downregulated in the dying cells,are present in an altered conformation or they are superseded by theupregulation of “eat-me” or pro-phagocytic signals. The cell surfaceprotein CD47 on healthy cells and its engagement of a phagocytereceptor, SIRPα, constitutes a key “don't eat-me” signal that can turnoff engulfment mediated by multiple modalities, including apoptotic cellclearance and FcR mediated phagocytosis. Blocking the CD47 mediatedengagement of SIRPα on a phagocyte can cause removal of live cellsbearing “eat me” signals.

CD47 is a broadly expressed transmembrane glycoprotein with a singleIg-like domain and five membrane spanning regions, which functions as acellular ligand for SIRPα with binding mediated through the NH2-terminalV-like domain of SIRPα. SIRPα is expressed primarily on myeloid cells,including macrophages, granulocytes, myeloid dendritic cells (DCs), mastcells, and their precursors, including hematopoietic stem cells.Structural determinants on SIRPα that mediate CD47 binding are discussedby Lee et al. (2007) J. Immunol. 179:7741-7750; Hatherley et al. (2007)J.B.C. 282:14567-75; and the role of SIRPα cis dimerization in CD47binding is discussed by Lee et al. (2010) J.B.C. 285:37953-63. Inkeeping with the role of CD47 to inhibit phagocytosis of normal cells,there is evidence that it is transiently upregulated on hematopoieticstem cells (HSCs) and progenitors just prior to and during theirmigratory phase, and that the level of CD47 on these cells determinesthe probability that they are engulfed in vivo.

Programmed cell death (PCD) and phagocytic cell removal are common waysthat an organism responds in order to remove damaged, precancerous, orinfected cells. Cells that survive this host response (e.g., cancerouscells, chronically infected cells, etc.) have devised ways to evade PCD,and/or phagocytic cell removal. CD47, the “don't eat me” signal, isconstitutively upregulated on a wide variety of diseased cells, cancercells, and infected cells, allowing these cells to evade phagocytosis.Anti-CD47 agents that block the interaction between CD47 on one cell(e.g., a cancer cell, an infected cell, etc.) and SIRPα on another cell(e.g., a phagocytic cell) counteract the increase of CD47 expression andfacilitate the phagocytosis of the cancer cell and/or the infected cell.Thus, anti-CD47 agents can be used to treat and/or protect against awide variety of conditions/disorders. In fact, anti-CD47 and anti-SIRPαblocking antibodies significantly increase phagocytosis of cancer cellsin vitro and in vivo. They have been shown to be effective at treatingmice engrafted with a wide range of human cancers, from leukemias tosolid tumors. However, in some cases an initial high dose of ananti-CD47 agent can cause a dose-dependent loss of red blood cells(RBCs) in mice and non-human primate (NHP) models by binding to CD47 onthe surface of the RBCs. The severity of this anemia can preclude theuse of higher doses that are required to achieve sustained serumconcentrations associated with therapeutic efficacy.

As an alternative to anti-CD47 agents, anti-SIRPα antibodies havepotential advantages relating to the relatively restriction expressionprofile with respect to cell types. Aspects of anti-SIRPα antibodies andthe use thereof are provided herein.

SUMMARY

Compositions and methods are provided relating to antibodies that bindto SIRPα and block the interaction between CD47 and SIRPα. Blocking theCD47-SIRPα pathway mediates phagocytosis of targeted cells, and cansynergize with other cell targeting agents, including without limitationcancer-specific antibodies; pathogen specific antibodies; and the like.Surprisingly it is shown that activity of an anti-SIRPα antibody oneffector cells may be substantially reduced when the antibodyproductively binds to an Fc receptor on the effector cell surface,including without limitation one or more of FcγRI; FcγRIIA; FcγRIIB1;FcγRIIB2; FcγRIIIA; FcγRIIIB receptors. The reduction in effectivenesscan result in inter-individual variation in patient responsiveness.Disabling productive Fc receptor engagement by reducing binding to oneor more Fc receptors other than FcRn, where the Fc receptor bindsmonomeric IgG and/or multimeric immune complexes, can restore activityto the antibody and provide an improved therapeutic profile.

In some embodiments, an antibody is provided comprising (i) a variableregion that specifically binds to SIRPα, e.g. human SIRPα, and (ii) anFc region with reduced binding to Fc receptors, including human Fcγreceptors, relative to a wild-type Fc region; or lacking a functional Fcregion. In some embodiments, the antibody specifically binds to humanSIRPα. In some embodiments the antibody binds to one or both of humanSIRP-β and human SIRPγ. In other embodiments the antibody lackssignificant binding to one or both of human SIRP-β and human SIRPγ. Insome embodiments the antibody specifically binds to the V1 and V2isotypes of human SIRPα. In some such embodiments, the Fc region is ahuman Fc region, where the Fc has been modified by one or more aminoacid changes to reduce Fc receptor binding. The antibody may be labeledwith a detectable label, immobilized on a solid phase and/or conjugatedwith a heterologous compound.

The antibody may also be provided as a bispecific or multispecificantibody reactive with a second antigen, particularly including cancerantigens, an immune checkpoint inhibitor, an immune costimulatoryagonist, antigens of chronic infection, etc. In some embodiments abispecific antibody has an active Fc region.

In some embodiments a humanized anti-SIRPα antibody is provided,comprising one or both of a heavy chain variable region as set forth inSEQ ID NO:1; and a light chain variable region sequence set forth in SEQID NO:2, or a biologically active variant derived therefrom. In someembodiments the antibody comprises an Fc region, which Fc region isoptionally an Fc region with reduced binding to Fc receptors. In otherembodiments the antibody lacks an Fc region, e.g. being provided as anF(ab)₂ antibody.

The compositions and methods of the invention can be used for thetreatment of human disease, where the anti-SIRPα antibody increasesphagocytosis of target cells, for example in combination with a secondantibody that binds to an antigen on the targeted cell surface.Phagocytic effector cells, including for example macrophages, express anumber of Fcγ receptors, and benefit from the use of an anti-SIRPαantibody having decreased FcR binding.

In some embodiments a pharmaceutical formulation is provided, e.g. foruse in the treatment of a human subject, where the formulation comprisesan antibody comprising (i) a variable region that specifically binds toSIRPα, e.g. human SIRPα, and (ii) an Fc region with reduced binding toFc receptors, e.g. human Fcγ receptors; or lacking a functional Fcregion. In some embodiments, the antibody specifically binds to humanSIRPα. In some embodiments the antibody binds to one or both of humanSIRP-β and human SIRPγ. In other embodiments the antibody lackssignificant binding to one or both of human SIRP-β and human SIRPγ. Insome embodiments the antibody specifically binds to the V1 and V2isotypes of human SIRPα. In some such embodiments, the Fc region is ahuman Fc region, where the Fc has been modified by one or more aminoacid changes to reduce Fc receptor binding. The pharmaceuticalformulation may comprise lyophilized antibody; and/or may comprise apharmaceutically acceptable excipient. The pharmaceutical formulationmay be provided as a unit dose, e.g. as a sterile pre-pack in a unitdose with diluent and delivery device, e.g. inhaler, syringe, etc.Pharmaceutical compositions or kits may further comprise a secondantibody that binds to a second antigen, e.g., a cancer cell marker, animmune checkpoint inhibitor, an immune costimulatory agonist, a markerof chronic infection, and the like.

The subject antibodies find use in various therapeutic methods, e.g. forthe treatment of diseases associated with CD47 in humans, e.g. cancer,chronic infection, atherosclerosis, aneurysm, etc. In some embodimentsof method of treatment is provided, comprising contacting an individualwith an effective dose of an antibody of the invention, wherein theeffective dose provides for binding the antibody of the invention to aphagocytic cell thereby increasing phagocytosis of target cellsexpressing CD47. Treatment may be systemic or localized, e.g. deliveryby intratumoral injection, etc.

The disclosure further provides: isolated nucleic acids encoding theantibodies and variants thereof; a vector comprising that nucleic acid,optionally operably linked to control sequences recognized by a hostcell transformed with the vector; a host cell comprising that vector; aprocess for producing the antibody comprising culturing the host cell sothat the nucleic acid is expressed and, optionally, recovering theantibody from the host cell culture (e.g. from the host cell culturemedium).

BRIEF DESCRIPTION OF THE DRAWINGS

The invention is best understood from the following detailed descriptionwhen read in conjunction with the accompanying drawings. The patent orapplication file contains at least one drawing executed in color. Copiesof this patent or patent application publication with color drawing(s)will be provided by the Office upon request and payment of the necessaryfee. It is emphasized that, according to common practice, the variousfeatures of the drawings are not to-scale. On the contrary, thedimensions of the various features are arbitrarily expanded or reducedfor clarity. Included in the drawings are the following figures.

FIG. 1 . Combination of anti-CD47 (Hu5F9-G4) or murine anti-SIRPalpha(mKWAR) antibodies with anti-CD20 (Rituximab) antibody enhances thephagocytosis of lymphoma cancer cells (Raji) compared to control IgG4antibody or monotherapy with Rituximab. Chimeric (mouse antigen bindingregion, human constant Fc region) antibody variants of KWAR with humanIgG1 or human IgG4 lower the phagocytosis enhancing effect compared to achimeric KWAR antibody with a dead Fc.

FIG. 2 , panels A-J. Determining synergy of variants of theanti-SIRPalpha antibody KWAR with rituximab to promotemacrophage-mediated phagocytosis of Raji lymphoma cells.

FIG. 3 , panels A-B. 9B11 and 7E11 synergize with rituximab to promotemacrophage-mediated phagocytosis of Raji cells.

FIG. 4 , panels A-B. Amino acid sequence of humanized KWAR (Panel A)heavy chain (SEQ ID NO:1) and (Panel B) light chain (SEQ ID NO:2).

FIG. 5 , panels A-B. Humanized Kwar synergizes with therapeuticantibodies to promote phagocytosis.

DETAILED DESCRIPTION

Before the present methods and compositions are described, it is to beunderstood that this invention is not limited to particular method orcomposition described, as such may, of course, vary. It is also to beunderstood that the terminology used herein is for the purpose ofdescribing particular embodiments only, and is not intended to belimiting, since the scope of the present invention will be limited onlyby the appended claims.

Where a range of values is provided, it is understood that eachintervening value, to the tenth of the unit of the lower limit unlessthe context clearly dictates otherwise, between the upper and lowerlimits of that range is also specifically disclosed. Each smaller rangebetween any stated value or intervening value in a stated range and anyother stated or intervening value in that stated range is encompassedwithin the invention. The upper and lower limits of these smaller rangesmay independently be included or excluded in the range, and each rangewhere either, neither or both limits are included in the smaller rangesis also encompassed within the invention, subject to any specificallyexcluded limit in the stated range. Where the stated range includes oneor both of the limits, ranges excluding either or both of those includedlimits are also included in the invention.

Unless defined otherwise, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention belongs. Although any methods andmaterials similar or equivalent to those described herein can be used inthe practice or testing of the present invention, some potential andpreferred methods and materials are now described. All publicationsmentioned herein are incorporated herein by reference to disclose anddescribe the methods and/or materials in connection with which thepublications are cited. It is understood that the present disclosuresupercedes any disclosure of an incorporated publication to the extentthere is a contradiction.

As will be apparent to those of skill in the art upon reading thisdisclosure, each of the individual embodiments described and illustratedherein has discrete components and features which may be readilyseparated from or combined with the features of any of the other severalembodiments without departing from the scope or spirit of the presentinvention. Any recited method can be carried out in the order of eventsrecited or in any other order which is logically possible.

It must be noted that as used herein and in the appended claims, thesingular forms “a”, “an”, and “the” include plural referents unless thecontext clearly dictates otherwise. Thus, for example, reference to “acell” includes a plurality of such cells and reference to “the peptide”includes reference to one or more peptides and equivalents thereof, e.g.polypeptides, known to those skilled in the art, and so forth.

The publications discussed herein are provided solely for theirdisclosure prior to the filing date of the present application. Nothingherein is to be construed as an admission that the present invention isnot entitled to antedate such publication by virtue of prior invention.Further, the dates of publication provided may be different from theactual publication dates which may need to be independently confirmed

The terms “treatment”, “treating”, “treat” and the like are used hereinto generally refer to obtaining a desired pharmacologic and/orphysiologic effect. The effect can be prophylactic in terms ofcompletely or partially preventing a disease or symptom(s) thereofand/or may be therapeutic in terms of a partial or completestabilization or cure for a disease and/or adverse effect attributableto the disease. The term “treatment” encompasses any treatment of adisease in a mammal, particularly a human, and includes: (a) preventingthe disease and/or symptom(s) from occurring in a subject who may bepredisposed to the disease or symptom but has not yet been diagnosed ashaving it; (b) inhibiting the disease and/or symptom(s), i.e., arrestingtheir development; or (c) relieving the disease symptom(s), i.e.,causing regression of the disease and/or symptom(s). Those in need oftreatment include those already inflicted (e.g., those with cancer,those with an infection, etc.) as well as those in which prevention isdesired (e.g., those with increased susceptibility to cancer, those withan increased likelihood of infection, those suspected of having cancer,those suspected of harboring an infection, etc.).

A therapeutic treatment is one in which the subject is inflicted priorto administration and a prophylactic treatment is one in which thesubject is not inflicted prior to administration. In some embodiments,the subject has an increased likelihood of becoming inflicted or issuspected of being inflicted prior to treatment. In some embodiments,the subject is suspected of having an increased likelihood of becominginflicted.

The terms “recipient”, “individual”, “subject”, “host”, and “patient”,are used interchangeably herein and refer to any mammalian subject forwhom diagnosis, treatment, or therapy is desired, particularly humans.“Mammal” for purposes of treatment refers to any animal classified as amammal, including humans, domestic and farm animals, and zoo, sports, orpet animals, such as dogs, horses, cats, cows, sheep, goats, pigs, etc.Preferably, the mammal is human.

As used in this invention, the term “epitope” means any antigenicdeterminant on an antigen to which the paratope of an antibody binds.Epitopic determinants usually consist of chemically active surfacegroupings of molecules such as amino acids or sugar side chains andusually have specific three dimensional structural characteristics, aswell as specific charge characteristics.

The word “label” when used herein refers to a detectable compound orcomposition which is conjugated directly or indirectly to the antibody.The label may itself be detectable by itself (e.g., radioisotope labelsor fluorescent labels) or, in the case of an enzymatic label, maycatalyze chemical alteration of a substrate compound or compositionwhich is detectable.

By “solid phase” is meant a non-aqueous matrix to which the antibody ofthe present invention can adhere. Examples of solid phases encompassedherein include those formed partially or entirely of glass (e.g.controlled pore glass), polysaccharides (e.g., agarose),polyacrylamides, polystyrene, polyvinyl alcohol and silicones. Incertain embodiments, depending on the context, the solid phase cancomprise the well of an assay plate; in others it is a purificationcolumn (e.g. an affinity chromatography column). This term also includesa discontinuous solid phase of discrete particles, such as thosedescribed in U.S. Pat. No. 4,275,149.

The terms “specific binding,” “specifically binds,” and the like, referto non-covalent or covalent preferential binding to a molecule relativeto other molecules or moieties in a solution or reaction mixture (e.g.,an antibody specifically binds to a particular polypeptide or epitoperelative to other available polypeptides). In some embodiments, theaffinity of one molecule for another molecule to which it specificallybinds is characterized by a K_(d) (dissociation constant) of 10⁻⁵ M orless (e.g., 10⁻⁶ M or less, 10⁻⁷ M or less, 10⁻⁸ M or less, 10⁻⁹ M orless, 10⁻¹⁰ M or less, 10⁻¹¹ M or less, 10⁻¹² M or less, 10⁻¹³ M orless, 10⁻¹⁴M or less, 10⁻¹⁵ M or less, or 10⁻¹⁶ M or less). “Affinity”refers to the strength of binding, increased binding affinity beingcorrelated with a lower K_(d).

The term “specific binding member” as used herein refers to a member ofa specific binding pair (i.e., two molecules, usually two differentmolecules, where one of the molecules, e.g., a first specific bindingmember, through non-covalent means specifically binds to the othermolecule, e.g., a second specific binding member).

Fc receptors. The human IgG receptor family consists of a number ofreceptors, including hFcγRI, hFcγRIIA, hFcγRIIC, hFcγRIIIA, hFcγRIIB,hFcγRIIIB. IgG also binds FcRn, which is involved in recycling andtransport of IgG. Activation of the Fc receptors may require the FcRsubunit to be expressed and functional at the cell surface. Other Fcreceptors include, for example, FcαRI (CD89), Fcα/μR, FcεRI, etc.Expression of the Fc receptors varies among immune effector cells.hFcγRI (CD64) is restricted to monocytes/macrophages and dendritic cells(DCs) and, inducibly, expressed on neutrophils and mast cells; hFcγRIIA(CD32A) is expressed on all myeloid cells but not on lymphocytes;hFcγRIIB (CD32B) is highly expressed only on circulating B cells andbasophils and expressed on tissue macrophages and DCs, but not on mastcells; hFcγRIIC (CD32C) is expressed on NK cells, monocytes, andneutrophils; hFcγRIIIA (CD16A) is expressed on NK cells andmonocytes/macrophages; hFcγRIIIB (CD16B) is expressed on neutrophils andsubsets of basophils.

FcRn, which importantly contributes to the biological half-life ofantibodies in the blood, is expressed on antigen-presenting cells,monocytes/macrophages, neutrophils, vascular endothelial cells,intestinal epithelial cells, and syncytiotrophoblasts.

The Fcγ receptors differ in their affinity for IgG and likewise thedifferent IgG subclasses have unique affinities for each of the Fcγreceptors. These interactions are further tuned by glycans(oligosaccharide), e.g. at position CH2-84.4 of IgG. For example, bycreating steric hindrance, fucose containing CH2-84.4 glycans reduce IgGaffinity for FcγRIIIA.

Fc domain or region. The Fc region of an antibody mediates its serumhalf-life and effector functions, such as complement-dependentcytotoxicity (CDC), antibody-dependent cellular cytotoxicity (ADCC) andantibody-dependent cell phagocytosis (ADCP). Engineering the Fc regionof a therapeutic monoclonal antibody or Fc fusion protein allows thegeneration of molecules that are better suited to the pharmacologyactivity required of them. The half-life of an IgG depends on itspH-dependent binding to the neonatal receptor FcRn. FcRn, which isexpressed on the surface of endothelial cells, binds the IgG in apH-dependent manner and protects it from degradation.

A “wild-type Fc region” possesses the effector functions of anative-sequence Fc region, in particular for the purposes of the presentinvention interacting with one or more of the Fc receptors such asFcγRI; FcγRIIA; FcγRIIB1; FcγRIIB2; FcγRIIIA; FcγRIIIB receptors; andcan be assessed using various assays as disclosed, for example, indefinitions herein. A “dead” Fc is one that has been mutagenized toretain activity with respect to, for example, prolonging serum half-lifethrough interaction with FcRn, but which has reduced or absent bindingto one or more other Fc receptor(s), including without limitation ahuman FcγR as listed above.

A “native-sequence Fc region” comprises an amino acid sequence identicalto the amino acid sequence of an Fc region found in nature.Native-sequence human Fc regions include a native-sequence human IgG1 Fcregion (non-A and A allotypes); native-sequence human IgG2 Fc region;native-sequence human IgG3 Fc region; and native-sequence human IgG4 Fcregion, as well as naturally occurring variants thereof.

A “variant Fc region” or “engineered Fc region” comprises an amino acidsequence that differs from that of a native-sequence Fc region by virtueof at least one amino acid modification, preferably one or more aminoacid substitution(s). Preferably, the variant Fc region has at least oneamino acid substitution compared to a native-sequence Fc region or tothe Fc region of a parent polypeptide, e.g., from about one to about tenamino acid substitutions, and preferably from about one to about fiveamino acid substitutions in a native-sequence Fc region or in the Fcregion of the parent polypeptide. The variant Fc region herein willpreferably possess at least about 80% homology with a native-sequence Fcregion and/or with an Fc region of a parent polypeptide, and mostpreferably at least about 90% homology therewith, more preferably atleast about 95% homology therewith.

Variant Fc sequences for a “dead Fc” may include three amino acidsubstitutions in the CH2 region to reduce FcγRI binding at EU indexpositions 234, 235, and 237 (see Duncan et al., (1988) Nature 332:563).Two amino acid substitutions in the complement C1q binding site at EUindex positions 330 and 331 reduce complement fixation (see Tao et al.,J. Exp. Med. 178:661 (1993) and Canfield and Morrison, J. Exp. Med.173:1483 (1991)). Substitution into human IgG1 of IgG2 residues atpositions 233-236 and IgG4 residues at positions 327, 330 and 331greatly reduces ADCC and CDC (see, for example, Armour K L. et al., 1999Eur J Immunol. 29(8):2613-24; and Shields R L. et al., 2001. J BiolChem. 276(9):6591-604).

Binding of IgG to the FcγRs or C1q depends on residues located in thehinge region and the CH2 domain. Two regions of the CH2 domain arecritical for FcγRs and C1q binding, and have unique sequences in IgG2and IgG4. Substitutions into human IgG1 or IgG2 residues at positions233-236 and IgG4 residues at positions 327, 330 and 331 have been shownto greatly reduce ADCC and CDC. Numerous mutations have been made in theCH2 domain of human IgG1.

The triple amino acid substitution L234A, L235A, and G237A largelyeliminates FcγR and complement effector functions (see, for example,US20100266505).

In some embodiments the Fc region has been modified by the choice ofexpression host, enzymatic treatment of amino acid substitutions to havereduced glycosylation and binding to FcγR, relative to the nativeprotein. Mutations that reduce binding to FcγR include, withoutlimitation, modification of the glycosylation on asparagine 297 of theFc domain, which is known to be required for optimal FcR interaction.For example known amino acid substitutions include N297 mutations, forexample N297A/Q/D/H/G/C, which changes result in the loss of aglycosylation site on the protein. Enzymatically deglycosylated Fcdomains, recombinantly expressed antibodies in the presence of aglycosylation inhibitor and the expression of Fc domains in bacteriahave a similar loss of glycosylation and consequent binding to FcγRs.

The LALA variant, L234A/L235A, also has significantly reduced FcγRbinding; as does E233P/L234V/L235A/G236+A327G/A330S/P331S. See, forexample, Armour et al. (1999) Eur J Immunol. 29(8):2613-24. The set ofmutations: K322A, L234A and L235A are sufficient to almost completelyabolish FcγR and C1q binding. A set of three mutations,L234F/L235E/P331S (dubbed TM), have a very similar effect.

Other Fc variants are possible, including without limitation one inwhich a region capable of forming a disulfide bond is deleted, or inwhich certain amino acid residues are eliminated at the N-terminal endof a native Fc form or a methionine residue is added thereto.

The Fc may be in the form of having native sugar chains, increased sugarchains compared to a native form or decreased sugar chains compared tothe native form, or may be in an aglycosylated or deglycosylated form.The increase, decrease, removal or other modification of the sugarchains may be achieved by methods common in the art, such as a chemicalmethod, an enzymatic method or by expressing it in a geneticallyengineered production cell line. Such cell lines can includemicroorganisms, e.g. Pichia Pastoris, and mammalians cell line, e.g. CHOcells, that naturally express glycosylating enzymes. Further,microorganisms or cells can be engineered to express glycosylatingenzymes, or can be rendered unable to express glycosylation enzymes (Seee.g., Hamilton, et al., Science, 313:1441 (2006); Kanda, et al, J.Biotechnology, 130:300 (2007); Kitagawa, et al., J. Biol. Chem., 269(27): 17872 (1994); Ujita-Lee et al., J. Biol. Chem., 264 (23): 13848(1989); Imai-Nishiya, et al, BMC Biotechnology 7:84 (2007); and WO07/055916). As one example of a cell engineered to have alteredsialylation activity, the alpha-2,6-sialyltransferase 1 gene has beenengineered into Chinese Hamster Ovary cells and into sf9 cells.Antibodies expressed by these engineered cells are thus sialylated bythe exogenous gene product. A further method for obtaining Fc moleculeshaving a modified amount of sugar residues compared to a plurality ofnative molecules includes separating said plurality of molecules intoglycosylated and non-glycosylated fractions, for example, using lectinaffinity chromatography (See e.g., WO 07/117505). The presence ofparticular glycosylation moieties has been shown to alter the functionof Immunoglobulins. For example, the removal of sugar chains from an Fcmolecule results in a sharp decrease in binding affinity to the C1q partof the first complement component C1 and a decrease or loss inantibody-dependent cell-mediated cytotoxicity (ADCC) orcomplement-dependent cytotoxicity (CDC), thereby not inducingunnecessary immune responses in vivo. Additional important modificationsinclude sialylation and fucosylation: the presence of sialic acid in IgGhas been correlated with anti-inflammatory activity (See e.g., Kaneko,et al, Science 313:760 (2006)), whereas removal of fucose from the IgGleads to enhanced ADCC activity (See e.g., Shoj-Hosaka, et al, J.Biochem., 140:777 (2006)).

The term “Fc-region-comprising antibody” refers to an antibody thatcomprises an Fc region. The C-terminal lysine (residue 447 according tothe EU numbering system) of the Fc region may be removed, for example,during purification of the antibody or by recombinant engineering thenucleic acid encoding the antibody. Accordingly, an antibody having anFc region according to this invention can comprise an antibody with orwithout K447.

Antibodies, also referred to as immunoglobulins, conventionally compriseat least one heavy chain and one light, where the amino terminal domainof the heavy and light chains is variable in sequence, hence is commonlyreferred to as a variable region domain, or a variable heavy (VH) orvariable light (VH) domain. The two domains conventionally associate toform a specific binding region, although as well be discussed here,specific binding can also be obtained with heavy chain only variablesequences, and a variety of non-natural configurations of antibodies areknown and used in the art.

A “therapeutic” antibody, as discussed herein, references an antibodythat is suitable for treatment of a patient, i.e. an antibody with invivo activity in a context appropriate for therapeutic use, e.g.treatment of a human subject. In some embodiments, a therapeuticantibody may refer to an antibody that binds to an antigen present onthe surface of a targeted cell, e.g. a tumor-specific antigen, apathogen-specific antigen, etc. Such therapeutic antibodies can becombined with an anti-SIRPα antibody to enhance phagocytosis of thetargeted cell.

The term “antibody” herein is used in the broadest sense andspecifically covers monoclonal antibodies, polyclonal antibodies,monomers, dimers, multimers, multispecific antibodies (e.g., bispecificantibodies), heavy chain only antibodies, three chain antibodies, singlechain Fv, nanobodies, etc., and also include antibody fragments, so longas they exhibit the desired biological activity (Miller et al (2003)Jour. of Immunology 170:4854-4861). For example, F(ab′)2 fragments areof interest as a format for anti-SIRPα antibodies. Antibodies may bemurine, human, humanized, chimeric, or derived from other species. Formany purposes the antibodies of the invention comprise a humanengineered Fc region.

The term antibody may reference a full-length heavy chain, a full lengthlight chain, an intact immunoglobulin molecule; or an immunologicallyactive portion of any of these polypeptides. The immunoglobulindisclosed herein can be of any type (e.g., IgG, IgE, IgM, IgD, and IgA),class (e.g., IgG1, IgG2, IgG3, IgG4, IgA1 and IgA2) or subclass ofimmunoglobulin molecule, including engineered subclasses with altered Fcportions that provide for reduced effector cell activity. Theimmunoglobulins can be derived from any species. In one aspect, theimmunoglobulin is of largely human origin, is humanized, or chimericwith respect to a human Fc region.

The term “variable” refers to the fact that certain portions of thevariable domains differ extensively in sequence among antibodies and areused in the binding and specificity of each particular antibody for itsparticular antigen. However, the variability is not evenly distributedthroughout the variable domains of antibodies. It is concentrated inthree segments called hypervariable regions both in the light chain andthe heavy chain variable domains. The more highly conserved portions ofvariable domains are called the framework regions (FRs). The variabledomains of native heavy and light chains each comprise four FRs, largelyadopting a beta-sheet configuration, connected by three hypervariableregions, which form loops connecting, and in some cases forming part of,the beta-sheet structure. The hypervariable regions in each chain areheld together in close proximity by the FRs and, with the hypervariableregions from the other chain, contribute to the formation of theantigen-binding site of antibodies (see Kabat et al (1991) Sequences ofProteins of Immunological Interest, 5th Ed. Public Health Service,National Institutes of Health, Bethesda, Md.).

The term “hypervariable region” when used herein refers to the aminoacid residues of an antibody which are responsible for antigen-binding.The hypervariable region may comprise amino acid residues from a“complementarity determining region” or “CDR”, and/or those residuesfrom a “hypervariable loop”. “Framework Region” or “FR” residues arethose variable domain residues other than the hypervariable regionresidues as herein defined.

Variable regions of interest include at least one CDR sequence from thevariable regions of an anti-SIRPα antibody, usually at least 2 CDRsequences, and more usually 3 CDR sequences on the light and on theheavy chain. One of skill in the art will understand that a number ofdefinitions of the CDRs are commonly in use, including the Kabatdefinition (see “Zhao et al. A germline knowledge based computationalapproach for determining antibody complementarity determining regions.”Mol Immunol. 2010; 47:694-700), which is based on sequence variabilityand is the most commonly used. The Chothia definition is based on thelocation of the structural loop regions (Chothia et al. “Conformationsof immunoglobulin hypervariable regions.” Nature. 1989; 342:877-883).Alternative CDR definitions of interest include, without limitation,those disclosed by Honegger, “Yet another numbering scheme forimmunoglobulin variable domains: an automatic modeling and analysistool.” J Mol Biol. 2001; 309:657-670; Ofran et al. “Automatedidentification of complementarity determining regions (CDRs) revealspeculiar characteristics of CDRs and B cell epitopes.” J Immunol. 2008;181:6230-6235; Almagro “Identification of differences in thespecificity-determining residues of antibodies that recognize antigensof different size: implications for the rational design of antibodyrepertoires.” J Mol Recognit. 2004; 17:132-143; and Padlanet al.“Identification of specificity-determining residues in antibodies.”Faseb J. 1995; 9:133-139., each of which is herein specificallyincorporated by reference.

The term “monoclonal antibody” as used herein refers to an antibodyobtained from a population of substantially homogeneous antibodies,i.e., the individual antibodies comprising the population are identicalexcept for possible naturally occurring mutations that may be present inminor amounts. Monoclonal antibodies are highly specific, being directedagainst a single antigenic site. Furthermore, in contrast to polyclonalantibody preparations, which include different antibodies directedagainst different determinants (epitopes), each monoclonal antibody isdirected against a single determinant on the antigen. In addition totheir specificity, the monoclonal antibodies are advantageous in thatthey may be synthesized uncontaminated by other antibodies. The modifier“monoclonal” indicates the character of the antibody as being obtainedfrom a substantially homogeneous population of antibodies, and is not tobe construed as requiring production of the antibody by any particularmethod.

The antibodies herein specifically include “chimeric” antibodies inwhich a portion of the heavy and/or light chain is identical with orhomologous to corresponding sequences in antibodies derived from aparticular species or belonging to a particular antibody class orsubclass, while the remainder of the chain(s) is identical with orhomologous to corresponding sequences in antibodies derived from anotherspecies or belonging to another antibody class or subclass, as well asfragments of such antibodies, so long as they exhibit the desiredbiological activity (U.S. Pat. No. 4,816,567; and Morrison et al (1984)Proc. Natl. Acad. Sci. USA, 81:6851-6855). Chimeric antibodies ofinterest herein include “primatized” antibodies comprising variabledomain antigen-binding sequences derived from a non-human primate (e.g.,Old World Monkey, Ape, etc.) and human constant region sequences.

An “intact antibody chain” as used herein is one comprising a fulllength variable region and a full length constant region. An intact“conventional” antibody comprises an intact light chain and an intactheavy chain, as well as a light chain constant domain (CL) and heavychain constant domains, CH1, hinge, CH2 and CH3 for secreted IgG. Otherisotypes, such as IgM or IgA may have different CH domains. The constantdomains may be native sequence constant domains (e.g., human nativesequence constant domains) or amino acid sequence variants thereof.

“Fv” is the minimum antibody fragment, which contains a completeantigen-recognition and antigen-binding site. The CD3 binding antibodiesof the invention comprise a dimer of one heavy chain and one light chainvariable domain in tight, non-covalent association; however additionalantibodies, e.g. for use in a multi-specific configuration, may comprisea VH in the absence of a VL sequence. Even a single variable domain (orhalf of an Fv comprising only three hypervariable regions specific foran antigen) has the ability to recognize and bind antigen, although theaffinity may be lower than that of two domain binding site.

The Fab fragment also contains the constant domain of the light chainand the first constant domain (CH1) of the heavy chain. Fab′ fragmentsdiffer from Fab fragments by the addition of a few residues at thecarboxy terminus of the heavy chain CH1 domain including one or morecysteines from the antibody hinge region. Fab′-SH is the designationherein for Fab′ in which the cysteine residue(s) of the constant domainsbear at least one free thiol group. F(ab′)₂ antibody fragmentsoriginally were produced as pairs of Fab′ fragments which have hingecysteines between them. Other chemical couplings of antibody fragmentsare also known.

“Humanized” forms of non-human (e.g., rodent) antibodies are chimericantibodies that contain minimal sequence derived from non-humanimmunoglobulin. See, for example, Jones et al, (1986) Nature321:522-525; Chothia et al (1989) Nature 342:877; Riechmann et al (1992)J. Mol. Biol. 224, 487-499; Foote and Winter, (1992) J. Mol. Biol.224:487-499; Presta et al (1993) J. Immunol. 151, 2623-2632; Werther etal (1996) J. Immunol. Methods 157:4986-4995; and Presta et al (2001)Thromb. Haemost. 85:379-389. For further details, see U.S. Pat. Nos.5,225,539; 6,548,640; 6,982,321; 5,585,089; 5,693,761; 6,407,213; Joneset al (1986) Nature, 321:522-525; and Riechmann et al (1988) Nature332:323-329.

Moreover, the term “antibody” as used herein, can refer in appropriateembodiments (unless otherwise stated or clear from context) to any ofthe art-known or developed constructs or formats for utilizing antibodystructural and functional features in alternative presentation. Forexample, embodiments, an antibody utilized in accordance with thepresent invention is in a format selected from, but not limited to,intact IgG, IgE and IgM, bi- or multi-specific antibodies (e.g.,Zybodies®, etc), single chain Fvs, polypeptide-Fc fusions, Fabs,cameloid antibodies, masked antibodies (e.g., Probodies®), Small ModularImmunoPharmaceuticals (“SMIPs™”), single chain or Tandem diabodies(TandAb®), VHHs, Anticalins®, Nanobodies®, minibodies, BiTE®s, ankyrinrepeat proteins or DARPINs®, Avimers®, a DART, a TCR-like antibody,Adnectins®, Affilins®, Trans-bodies®, Affibodies®, a TrimerX®,MicroProteins, Fynomers®, Centyrins®, and a KALBITOR®. In someembodiments, an antibody may lack a covalent modification (e.g.,attachment of a glycan) that it would have if produced naturally. Insome embodiments, an antibody may contain a covalent modification (e.g.,attachment of a glycan, a payload, e.g., a detectable moiety, atherapeutic moiety, a catalytic moiety, etc., or other pendant group[e.g., poly-ethylene glycol, etc.

Exemplary antibody agents include, but are not limited to, humanantibodies, primatized antibodies, chimeric antibodies, bi-specificantibodies, humanized antibodies, conjugated antibodies (i.e.,antibodies conjugated or fused to other proteins, radiolabels,cytotoxins), Small Modular ImmunoPharmaceuticals (“SMIPs™”), singlechain antibodies, cameloid antibodies, and antibody fragments. As usedherein, the term “antibody agent” also includes intact monoclonalantibodies, polyclonal antibodies, single domain antibodies (e.g., sharksingle domain antibodies (e.g., IgNAR or fragments thereof)),multispecific antibodies (e.g. bi-specific antibodies) formed from atleast two intact antibodies, and antibody fragments so long as theyexhibit the desired biological activity. In some embodiments, the termencompasses stapled peptides. In some embodiments, the term encompassesone or more antibody-like binding peptidomimetics. In some embodiments,the term encompasses one or more antibody-like binding scaffoldproteins. In come embodiments, the term encompasses monobodies oradnectins.

“Antibody fragment”, and all grammatical variants thereof, as usedherein are defined as a portion of an intact antibody comprising theantigen binding site or variable region of the intact antibody, whereinthe portion is free of the constant heavy chain domains (i.e. CH2, CH3,and CH4, depending on antibody isotype) of the Fc region of the intactantibody. Examples of antibody fragments include Fab, Fab′, Fab′-SH,F(ab′)₂, and Fv fragments; diabodies; any antibody fragment that is apolypeptide having a primary structure consisting of one uninterruptedsequence of contiguous amino acid residues (referred to herein as a“single-chain antibody fragment” or “single chain polypeptide”),including without limitation (1) single-chain Fv (scFv) molecules (2)single chain polypeptides containing only one light chain variabledomain, or a fragment thereof that contains the three CDRs of the lightchain variable domain, without an associated heavy chain moiety and (3)single chain polypeptides containing only one heavy chain variableregion, or a fragment thereof containing the three CDRs of the heavychain variable region, without an associated light chain moiety; andmultispecific or multivalent structures formed from antibody fragments.In an antibody fragment comprising one or more heavy chains, the heavychain(s) can contain any constant domain sequence (e.g. CH1 in the IgGisotype) found in a non-Fc region of an intact antibody, and/or cancontain any hinge region sequence found in an intact antibody, and/orcan contain a leucine zipper sequence fused to or situated in the hingeregion sequence or the constant domain sequence of the heavy chain(s).

Unless specifically indicated to the contrary, the term “conjugate” asdescribed and claimed herein is defined as a heterogeneous moleculeformed by the covalent attachment of one or more antibody fragment(s) toone or more polymer molecule(s), wherein the heterogeneous molecule iswater soluble, i.e. soluble in physiological fluids such as blood, andwherein the heterogeneous molecule is free of any structured aggregate.A conjugate of interest is PEG. In the context of the foregoingdefinition, the term “structured aggregate” refers to (1) any aggregateof molecules in aqueous solution having a spheroid or spheroid shellstructure, such that the heterogeneous molecule is not in a micelle orother emulsion structure, and is not anchored to a lipid bilayer,vesicle or liposome; and (2) any aggregate of molecules in solid orinsolubilized form, such as a chromatography bead matrix, that does notrelease the heterogeneous molecule into solution upon contact with anaqueous phase. Accordingly, the term “conjugate” as defined hereinencompasses the aforementioned heterogeneous molecule in a precipitate,sediment, bioerodible matrix or other solid capable of releasing theheterogeneous molecule into aqueous solution upon hydration of thesolid.

The anti-SIRPα antibodies herein specifically include “chimeric”antibodies (immunoglobulins) in which a portion of the heavy and/orlight chain is identical with or homologous to corresponding sequencesin antibodies derived from a particular species or belonging to aparticular antibody class or subclass, while the remainder of thechain(s) is identical with or homologous to corresponding sequences inantibodies derived from another species or belonging to another antibodyclass or subclass, as well as fragments of such antibodies, so long asthey exhibit the desired biological activity.

An “isolated” antibody is one which has been identified and separatedand/or recovered from a component of its natural environment.Contaminant components of its natural environment are materials whichwould interfere with diagnostic or therapeutic uses for the antibody,and may include enzymes, hormones, and other proteinaceous ornonproteinaceous solutes. In some embodiments, the antibody will bepurified (1) to greater than 75% by weight of antibody as determined bythe Lowry method, and most preferably more than 80%, 90% or 99% byweight, or (2) to homogeneity by SDS-PAGE under reducing or nonreducingconditions using Coomassie blue or, preferably, silver stain. Isolatedantibody includes the antibody in situ within recombinant cells since atleast one component of the antibody's natural environment will not bepresent. Ordinarily, however, isolated antibody will be prepared by atleast one purification step.

The term “epitope tagged” when used herein refers to an anti-SIRPαantibody (or fragment) fused to an “epitope tag”. The epitope tagpolypeptide has enough residues to provide an epitope against which anantibody can be made, yet is short enough such that it does notinterfere with activity of the anti-SIRPα antibody. The epitope tagpreferably is sufficiently unique so that the antibody specific for theepitope does not substantially cross-react with other epitopes. Suitabletag polypeptides generally have at least 6 amino acid residues andusually between about 8-50 amino acid residues (preferably between about9-30 residues). Examples include the c-myc tag and the 8F9, 3C7, 6E10,G4, B7 and 9E10 antibodies thereto (Evan et al., Mol. Cell. Biol.5(12):3610-3616 (1985)); and the Herpes Simplex virus glycoprotein D(gD) tag and its antibody (Paborsky et al., Protein Engineering3(6):547-553 (1990)). An additional example is a “histidine tag” or“histidine-rich affinity peptide”, which is a metal ion affinity peptidethat is rich in histidines (e.g., 6xHis tag, HAT tag, 6xHN tag, and thelike). A histidine tag can also specifically bind to an anti-Hisantibody.

SIRPα1 (PTPNS1, SHPS1), is a transmembrane glycoprotein, expressedprimarily on myeloid and neuronal cells. SIRPα interacts with the widelydistributed membrane protein CD47. In addition to SIRPα, there are twoclosely related proteins in the SIRP family: SIRPβ and SIRPγ. All threehave three immunoglobulin superfamily (IgSF) domains in theirextracellular region. In humans, the SIRPα protein is found in two majorforms. One form, the variant 1 or V1 form, has the amino acid sequenceset out as NCBI RefSeq NP_542970.1 (residues 27-504 constitute themature form). Another form, the variant 2 or V2 form, differs by 13amino acids and has the amino acid sequence set out in GenBank asCAA71403.1 (residues 30-504 constitute the mature form). These two formsof SIRPα constitute about 80% of the forms of SIRPα present in humans,and both are embraced herein by the term “human SIRPα”. Also embraced bythe term “human SIRPα” are the minor forms thereof that are endogenousto humans and have the same property of triggering signal transductionthrough CD47 upon binding thereto. Sequences of human SIRPα variants maybe accessed through public databases, including Genbank accessionnumbers: ref|NP_542970.1; gb|EAX10606.1; ref|XP_005260726.1;gb|EAX10606.1; XP_005260726.1; gb|EAX10611.1; gb|EAX10609.1;dbj|BAA12974.1; gb|AAH26692.1; ref|XP_011527475.1. See, for example Leeet al. (2007) J. Immunol. 179(11):7741-7750; herein specificallyincorporated by reference.

Antibodies that specifically bind to human SIRPα are known and used inthe art, and may be adapted by the use of an engineered Fc region asdisclosed herein. Exemplary antibodies include those described ininternational patent application WO 2015/138600; in published USapplication 2014/0242095 (University Health Networks); publishedapplication CN103665165 (JIANGSU KUANGYA BIOLOGICAL MEDICAL SCIENCE &TECHNOLOGY; Zhao X W et al. Proc Natl Acad Sci U S A 108:18342-7 (2011),each herein specifically incorporated by reference. An anti-SIRPαantibody may be pan-specific, i.e. binding to two or more differenthuman SIRPα isoforms; or may be specific for one isoform. For example,the antibody 1.23A described by Zhang et al., supra. is reported to bespecific for the SIRPα1 variant, while the 12C4 antibody ispan-specific. Anti-SIRPα antibodies can also be specific for SIRPα andlack binding to SIRPβ and/or SIRPγ. Anti-SIRPa antibodies can bepan-specific with respect to SIRPβ and/or SIRPγ.

The terms “co-administration”, “co-administer”, and “in combinationwith” include the administration of two or more therapeutic agentseither simultaneously, concurrently or sequentially within no specifictime limits. In one embodiment, the agents are present in the cell or inthe subjects body at the same time or exert their biological ortherapeutic effect at the same time. In one embodiment, the therapeuticagents are in the same composition or unit dosage form. In otherembodiments, the therapeutic agents are in separate compositions or unitdosage forms. In certain embodiments, a first agent can be administeredprior to (e.g., minutes, 15 minutes, 30 minutes, 45 minutes, 1 hour, 2hours, 4 hours, 6 hours, 12 hours, 24 hours, 48 hours, 72 hours, 96hours, 1 week, 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 8 weeks, or12 weeks before), concomitantly with, or subsequent to (e.g., 5 minutes,15 minutes, 30 minutes, 45 minutes, 1 hour, 2 hours, 4 hours, 6 hours,12 hours, 24 hours, 48 hours, 72 hours, 96 hours, 1 week, 2 weeks, 3weeks, 4 weeks, 5 weeks, 6 weeks, 8 weeks, or 12 weeks after) theadministration of a second therapeutic agent.

Anti-SIRPα antibodies may be used therapeutically in combination with asecond antibody or agent that selectively binds to a target cell. Theterm “target cell” can be used in different ways depending on context.Typically a “target cell” is a cell that will be phagocytosed by aphagocytic cell (e.g., a phagocyte), where the phagocytosis is enhancedas a result of administering a subject anti-SIRPα antibody. Thus, theterm “target cell” can refer to a CD47-expressing cell, because asubject anti-SIRPα antibody, by inhibiting the interaction between theCD47-expressing cell and the SIRPα expressing phagocytic cell,facilitates phagocytosis of the CD47-expressing cell.

However, in some cases, the target cell need not express high levels ofCD47 (and in some cases need not express CD47 at all) in order for asubject multispecific antibody to induce phagocytosis of the targetcell. For example, in the context of a multispecific (e.g., bispecific)antibody, the SIRPα binding region (the first binding region) of asubject multispecific (e.g., bispecific) antibody binds to SIRPα on aphagocytic cell (e.g., a macrophage), which allows the multispecificantibody to function as a tether to bring the phagocytic cell into thevicinity of a cell expressing an antigen (e.g., a marker of a cancercell) that is recognized by (specifically bound by) a second bindingregion of the multispecific antibody (e.g., the second binding region ofa bispecific antibody). Therefore, in the context of a multispecificantibody, a target cell can be a cell that does not express high levelsof CD47 (and can also be a cell that does not express CD47). In someembodiments, a target cell is a mammalian cell, for example a humancell. A target cell can be from any individual (e.g., patient, subject,and the like) as described below.

In some cases, a target cell is an “inflicted” cell (e.g., a cell froman “inflicted” individual), where the term “inflicted” is used herein torefer to a subject with symptoms, an illness, or a disease that can betreated with a subject anti-SIRPα antibody. An “inflicted” subject canhave cancer, can harbor an infection (e.g., a chronic infection), and/orcan have other hyper-proliferative conditions, for example sclerosis,fibrosis, and the like, etc. Also of interest is the use in thetreatment of cardiovascular conditions, including without limitationaneurysm, atherosclerosis, etc. “Inflicted cells” can be those cellsthat cause the symptoms, illness, or disease. As non-limiting examples,the inflicted cells of an inflicted patient can be CD47 expressingcancer cells, infected cells, inflammatory cells, immune cells, and thelike. One indication that an illness or disease can be treated with asubject anti-SIRPα antibody is that the involved cells (i.e., theinflicted cells, e.g., the cancerous cells, the infected cells, theinflammatory cells, the immune cells, etc.) express CD47 (e.g., in somecases, an increased level of CD47 compared to normal cells of the samecell type).

For the treatment of cancer, the anti-SIRPα antibody may be combinedwith one or more antibodies specific for a tumor antigen. Of these,tumor-associated antigens (TAAs) are relatively restricted to tumorcells, whereas tumor-specific antigens (TSAs) are unique to tumor cells.TSAs and TAAs typically are portions of intracellular moleculesexpressed on the cell surface as part of the major histocompatibilitycomplex.

Tissue specific differentiation antigens are molecules present on tumorcells and their normal cell counterparts. Tumor-associated antigensknown to be recognized by therapeutic mAbs fall into several differentcategories. Hematopoietic differentiation antigens are glycoproteinsthat are usually associated with cluster of differentiation (CD)groupings and include CD20, CD30, CD33 and CD52. Cell surfacedifferentiation antigens are a diverse group of glycoproteins andcarbohydrates that are found on the surface of both normal and tumorcells. Antigens that are involved in growth and differentiationsignaling are often growth factors and growth factor receptors. Growthfactors that are targets for antibodies in cancer patients include CEA,epidermal growth factor receptor (EGFR; also known as ERBB1)′ ERBB2(also known as HER2), ERBB3, MET (also known as HGFR), insulin-likegrowth factor 1 receptor (IGF1 R), ephrin receptor A3 (EPHA3), tumornecrosis factor (TNF)-related apoptosis-inducing ligand receptor 1(TRAILR1; also known as TNFRSF10A), TRAILR2 (also known as TNFRSF10B)and receptor activator of nuclear factor-κB ligand (RANKL; also known asTNFSF11). Antigens involved in angiogenesis are usually proteins orgrowth factors that support the formation of new microvasculature,including vascular endothelial growth factor (VEGF), VEGF receptor(VEGFR), integrin αVβ3 and integrin α5β1. Tumor stroma and theextracellular matrix are indispensable support structures for a tumor.Stromal and extracellular matrix antigens that are therapeutic targetsinclude fibroblast activation protein (FAP) and tenascin.

Examples of therapeutic antibodies useful in bispecific configurationsor as combination therapy include, without limitation, rituximab;Ibritumomab; tiuxetan; tositumomab; Brentuximab; vedotin; Gemtuzumab;ozogamicin; Alemtuzumab; IGN101; adecatumumab; Labetuzumab; huA33;Pemtumomab; oregovomab; CC49 (minretumomab); cG250; J591; MOv18;MORAb-003 (farletuzumab); 3F8, ch14.18; KW-2871; hu3S193; IgN311;Bevacizumab; IM-2C6; CDP791; Etaracizumab; Volociximab; Cetuximab,panitumumab, nimotuzumab; 806; Trastuzumab; pertuzumab; MM-121; AMG 102,METMAB; SCH 900105; AVE1642, IMC-A12, MK-0646, R1507; CP 751871; KB004;IIIA4; Mapatumumab (HGS-ETR1); HGS-ETR2; CS-1008; Denosumab;Sibrotuzumab; F19; and 81C6. A bispecific antibody may use the Fc regionthat activates an Fcγ receptor.

For the treatment of cancer, the anti-SIRPα antibody may be combinedwith one or more antibodies that inhibit immune checkpoint proteins. Ofparticular interest are immune checkpoint proteins displayed on thesurface of a tumor cell. The immune-checkpoint receptors that have beenmost actively studied in the context of clinical cancer immunotherapy,cytotoxic T-lymphocyte-associated antigen 4 (CTLA4; also known as CD152)and programmed cell death protein 1 (PD1; also known as CD279)—are bothinhibitory receptors. The clinical activity of antibodies that blockeither of these receptors implies that antitumor immunity can beenhanced at multiple levels and that combinatorial strategies can beintelligently designed, guided by mechanistic considerations andpreclinical models.

The two ligands for PD1 are PD1 ligand 1 (PDL1; also known as B7-H1 andCD274) and PDL2 (also known as B7-DC and CD273). PDL1 is expressed oncancer cells and through binding to its receptor PD1 on T cells itinhibits T cell activation/function. See, for example, Avelumab as atherapeutic antibody.

Agents that agonize an immune costimulatory molecule are also useful inthe methods of the invention. Such agents include agonists or CD40 andOX40. CD40 is a costimulatory protein found on antigen presenting cells(APCs) and is required for their activation. These APCs includephagocytes (macrophages and dendritic cells) and B cells. CD40 is partof the TNF receptor family. The primary activating signaling moleculesfor CD40 are IFNγ and CD40 ligand (CD40L). Stimulation through CD40activates macrophages.

Anti CCR4 (CD194) antibodies of interest include humanized monoclonalantibodies directed against C-C chemokine receptor 4 (CCR4) withpotential anti-inflammatory and antineoplastic activities.

Examples of symptoms, illnesses, and/or diseases that can be treatedwith a subject anti-SIRPα antibody include, but are not limited tocancer (any form of cancer, including but not limited to: carcinomas,soft tissue tumors, sarcomas, teratomas, melanomas, leukemias,lymphomas, brain cancers, solid tumors, mesothelioma (MSTO), etc.);infection (e.g., chronic infection); and an immunological disease ordisorder (e.g., an inflammatory disease)(e.g., multiple sclerosis,arthritis, and the like, e.g., for immunosuppressive therapy). A subjectanti-SIRPα antibody can also be used for transplant conditioning (e.g.,stem cell transplant, bone marrow transplant, etc.) (e.g., to destroymalignant cells, to provide immunosuppression to prevent the patient'sbody from rejecting the donor's cells/stem cells, etc.). For example, insome cases, a subject antibody combination or bispecific antibody (e.g.,anti-SIRPα in combination with anti-CD117) finds use for transplantconditioning. For example, a subject antibody combination or bispecificantibody (e.g., anti-SIRPα in combination with anti-CD117) can be usedfor bone marrow transplant conditioning. In some cases, a subjectanti-SIRPα antibody (e.g., an antibody combination) can be used forimmunosuppressive therapy.

For example, any cancer, where the cancer cells exhibit increasedexpression of CD47 compared to non-cancer cells, is a suitable cancer tobe treated by the subject methods and compositions. As used herein“cancer” includes any form of cancer, including but not limited to solidtumor cancers (e.g., lung, prostate, breast, bladder, colon, ovarian,pancreas, kidney, liver, glioblastoma, medulloblastoma, leiomyosarcoma,head & neck squamous cell carcinomas, melanomas, neuroendocrine; etc.)and liquid cancers (e.g., hematological cancers); carcinomas; softtissue tumors; sarcomas; teratomas; melanomas; leukemias; lymphomas; andbrain cancers, including minimal residual disease, and including bothprimary and metastatic tumors. Any cancer, where the cancer cellsexpress CD47 (e.g., in some cases, the cancer cells exhibit increasedexpression of CD47 compared to non-cancer cells), is a suitable cancerto be treated by the subject methods and compositions (e.g., a subjectanti-SIRPα antibody).

Carcinomas are malignancies that originate in the epithelial tissues.Epithelial cells cover the external surface of the body, line theinternal cavities, and form the lining of glandular tissues. Examples ofcarcinomas include, but are not limited to: adenocarcinoma (cancer thatbegins in glandular (secretory) cells), e.g., cancers of the breast,pancreas, lung, prostate, and colon can be adenocarcinomas;adrenocortical carcinoma; hepatocellular carcinoma; renal cellcarcinoma; ovarian carcinoma; carcinoma in situ; ductal carcinoma;carcinoma of the breast; basal cell carcinoma; squamous cell carcinoma;transitional cell carcinoma; colon carcinoma; nasopharyngeal carcinoma;multilocular cystic renal cell carcinoma; oat cell carcinoma; large celllung carcinoma; small cell lung carcinoma; non-small cell lungcarcinoma; and the like. Carcinomas may be found in prostrate, pancreas,colon, brain (usually as secondary metastases), lung, breast, skin, etc.

Soft tissue tumors are a highly diverse group of rare tumors that arederived from connective tissue. Examples of soft tissue tumors include,but are not limited to: alveolar soft part sarcoma; angiomatoid fibroushistiocytoma; chondromyoxid fibroma; skeletal chondrosarcoma;extraskeletal myxoid chondrosarcoma; clear cell sarcoma; desmoplasticsmall round-cell tumor; dermatofibrosarcoma protuberans; endometrialstromal tumor; Ewing's sarcoma; fibromatosis (Desmoid); fibrosarcoma,infantile; gastrointestinal stromal tumor; bone giant cell tumor;tenosynovial giant cell tumor; inflammatory myofibroblastic tumor;uterine leiomyoma; leiomyosarcoma; lipoblastoma; typical lipoma; spindlecell or pleomorphic lipoma; atypical lipoma; chondroid lipoma;well-differentiated liposarcoma; myxoid/round cell liposarcoma;pleomorphic liposarcoma; myxoid malignant fibrous histiocytoma;high-grade malignant fibrous histiocytoma; myxofibrosarcoma; malignantperipheral nerve sheath tumor; mesothelioma; neuroblastoma;osteochondroma; osteosarcoma; primitive neuroectodermal tumor; alveolarrhabdomyosarcoma; embryonal rhabdomyosarcoma; benign or malignantschwannoma; synovial sarcoma; Evan's tumor; nodular fasciitis;desmoid-type fibromatosis; solitary fibrous tumor; dermatofibrosarcomaprotuberans (DFSP); angiosarcoma; epithelioid hemangioendothelioma;tenosynovial giant cell tumor (TGCT); pigmented villonodular synovitis(PVNS); fibrous dysplasia; myxofibrosarcoma; fibrosarcoma; synovialsarcoma; malignant peripheral nerve sheath tumor; neurofibroma; andpleomorphic adenoma of soft tissue; and neoplasias derived fromfibroblasts, myofibroblasts, histiocytes, vascular cells/endothelialcells and nerve sheath cells.

A sarcoma is a rare type of cancer that arises in cells of mesenchymalorigin, e.g., in bone or in the soft tissues of the body, includingcartilage, fat, muscle, blood vessels, fibrous tissue, or otherconnective or supportive tissue. Different types of sarcoma are based onwhere the cancer forms. For example, osteosarcoma forms in bone,liposarcoma forms in fat, and rhabdomyosarcoma forms in muscle. Examplesof sarcomas include, but are not limited to: askin's tumor; sarcomabotryoides; chondrosarcoma; ewing's sarcoma; malignanthemangioendothelioma; malignant schwannoma; osteosarcoma; and softtissue sarcomas (e.g., alveolar soft part sarcoma; angiosarcoma;cystosarcoma phyllodesdermatofibrosarcoma protuberans (DFSP); desmoidtumor; desmoplastic small round cell tumor; epithelioid sarcoma;extraskeletal chondrosarcoma; extraskeletal osteosarcoma; fibrosarcoma;gastrointestinal stromal tumor (GIST); hemangiopericytoma;hemangiosarcoma (more commonly referred to as “angiosarcoma”); kaposi'ssarcoma; leiomyosarcoma; liposarcoma; lymphangiosarcoma; malignantperipheral nerve sheath tumor (MPNST); neurofibrosarcoma; synovialsarcoma; undifferentiated pleomorphic sarcoma, and the like).

A teratomas is a type of germ cell tumor that may contain severaldifferent types of tissue (e.g., can include tissues derived from anyand/or all of the three germ layers: endoderm, mesoderm, and ectoderm),including for example, hair, muscle, and bone. Teratomas occur mostoften in the ovaries in women, the testicles in men, and the tailbone inchildren.

Melanoma is a form of cancer that begins in melanocytes (cells that makethe pigment melanin). It may begin in a mole (skin melanoma), but canalso begin in other pigmented tissues, such as in the eye or in theintestines.

Leukemias are cancers that start in blood-forming tissue, such as thebone marrow, and causes large numbers of abnormal blood cells to beproduced and enter the bloodstream. For example, leukemias can originatein bone marrow-derived cells that normally mature in the bloodstream.Leukemias are named for how quickly the disease develops and progresses(e.g., acute versus chronic) and for the type of white blood cell thatis effected (e.g., myeloid versus lymphoid). Myeloid leukemias are alsocalled myelogenous or myeloblastic leukemias. Lymphoid leukemias arealso called lymphoblastic or lymphocytic leukemia. Lymphoid leukemiacells may collect in the lymph nodes, which can become swollen. Examplesof leukemias include, but are not limited to: Acute myeloid leukemia(AML), Acute lymphoblastic leukemia (ALL), Chronic myeloid leukemia(CML), and Chronic lymphocytic leukemia (CLL).

Lymphomas are cancers that begin in cells of the immune system. Forexample, lymphomas can originate in bone marrow-derived cells thatnormally mature in the lymphatic system. There are two basic categoriesof lymphomas. One kind is Hodgkin lymphoma (HL), which is marked by thepresence of a type of cell called the Reed-Sternberg cell. There arecurrently 6 recognized types of HL. Examples of Hodgkin lymphomasinclude: nodular sclerosis classical Hodgkin lymphoma (CHL), mixedcellularity CHL, lymphocyte-depletion CHL, lymphocyte-rich CHL, andnodular lymphocyte predominant HL.

The other category of lymphoma is non-Hodgkin lymphomas (NHL), whichincludes a large, diverse group of cancers of immune system cells.Non-Hodgkin lymphomas can be further divided into cancers that have anindolent (slow-growing) course and those that have an aggressive(fast-growing) course. There are currently 61 recognized types of NHL.Examples of non-Hodgkin lymphomas include, but are not limited to:AIDS-related Lymphomas, anaplastic large-cell lymphoma,angioimmunoblastic lymphoma, blastic NK-cell lymphoma, Burkitt'slymphoma, Burkitt-like lymphoma (small non-cleaved cell lymphoma),chronic lymphocytic leukemia/small lymphocytic lymphoma, cutaneousT-Cell lymphoma, diffuse large B-Cell lymphoma, enteropathy-type T-Celllymphoma, follicular lymphoma, hepatosplenic gamma-delta T-Celllymphomas, T-Cell leukemias, lymphoblastic lymphoma, mantle celllymphoma, marginal zone lymphoma, nasal T-Cell lymphoma, pediatriclymphoma, peripheral T-Cell lymphomas, primary central nervous systemlymphoma, transformed lymphomas, treatment-related T-Cell lymphomas, andWaldenstrom's macroglobulinemia.

Brain cancers include any cancer of the brain tissues. Examples of braincancers include, but are not limited to: gliomas (e.g., glioblastomas,astrocytomas, oligodendrogliomas, ependymomas, and the like),meningiomas, pituitary adenomas, vestibular schwannomas, primitiveneuroectodermal tumors (medulloblastomas), etc.

As used herein, the term “infection” refers to any state in at least onecell of an organism (i.e., a subject) is infected by an infectious agent(e.g., a subject has an intracellular pathogen infection, e.g., achronic intracellular pathogen infection). As used herein, the term“infectious agent” refers to a foreign biological entity (i.e. apathogen) that induces CD47 expression (e.g., increased CD47 expression)in at least one cell of the infected organism. For example, infectiousagents include, but are not limited to bacteria, viruses, protozoans,and fungi. Intracellular pathogens are of particular interest.Infectious diseases are disorders caused by infectious agents. Someinfectious agents cause no recognizable symptoms or disease undercertain conditions, but have the potential to cause symptoms or diseaseunder changed conditions. The subject methods can be used in thetreatment of chronic pathogen infections, for example including but notlimited to viral infections, e.g. retrovirus, lentivirus, hepadna virus,herpes viruses, pox viruses, human papilloma viruses, etc.;intracellular bacterial infections, e.g. Mycobacterium, Chlamydophila,Ehrlichia, Rickettsia, Brucella, Legionella, Francisella, Listeria,Coxiella, Neisseria, Salmonella, Yersinia sp, Helicobacter pylori etc.;and intracellular protozoan pathogens, e.g. Plasmodium sp, Trypanosomasp., Giardia sp., Toxoplasma sp., Leishmania sp., etc.

Also of interest for treatment with anti-SIRPα antibodies is theprevention and treatment of coronary artery disease (CAD) in a subject,including without limitation methods of preventing or treatingatherosclerosis, aneurysm, etc., for example as described in patentpublications WO 2015/041987; WO 2016/138306; WO 2016/044021, each hereinspecifically incorporated by reference.

Polypeptides

In one aspect, the present disclosure is directed to antibodies (andcell lines that produce such antibodies) that specifically bind humanSIRPα (i.e., an anti-SIRPα antibody) and reduce the interaction betweenCD47 on one cell (e.g., a cancerous cell, an infected cell, etc.) andSIRPα on another cell (e.g., a phagocytic cell). The antibody comprises(i) a variable region that specifically binds to SIRPα, e.g. humanSIRPα, and (ii) an Fc region with reduced binding to one or more Fcreceptors other than FcRn, including human Fcγ receptors; or lacks an Fcregion. In such embodiments, the Fc region is a human Fc region, wherethe Fc has been modified, or engineered, by one or more amino acidchanges to reduce Fc receptor binding. Specific anti-SIRPαantibodiesinclude, without limitation, KWAR23, which antibody is disclosed hereinin a chimeric and humanized format.

The antibody may also be provided as a bispecific or multispecificantibody reactive with a second antigen, particularly including cancerantigens, an immune checkpoint inhibitor, an immune costimulatoryagonist, antigens of chronic infection, etc. Anti-SIRPα antibodies canbind SIRPα without inhibiting phagocytosis (activating or stimulatingsignaling through SIRPα inhibits phagocytosis). In other words,anti-SIRPα antibodies may bind SIRPα, but block CD47-induced SIRPαsignaling. Thus, suitable anti-SIRPα antibodies facilitate thepreferential phagocytosis of inflicted cells (e.g., cancerous cells,infected cells, etc.) over normal cells by inhibiting CD47-induced SIRPαsignaling, with reduced binding to an FcR present on effector cells,particularly present on human macrophages.

Data provided herein indicate that activity e.g. in enhancingphagocytosis when combined with a cell-targeted antibody, of ananti-SIRPα antibody comprising an wild-type human Fc region such as anIgG4 or IgG1 region can show inter-individual variability. Inparticular, some individuals (responders) respond by a synergisticincrease in phagocytosis, while other individuals (non-responders) lacka significant enhancement of phagocytosis. The number of non-respondersin a population will vary with the composition of the population, butmay be up to about 10%, up to about 20%, up to about 30%, up to about40%, up to about 50%, up to about 60%, up to about 70%, up to about 80%,up to about 90% or more. For clinical purposes it is undesirable to havenon-responders in the population. Use of an anti-SIRPα antibody thatcomprises a “dead” Fc, i.e. a human Fc sequence engineered to havereduced binding to one or more human FcR other than FcRn, reduces thenumber of non-responders in a population, e.g. reducing the number ofnon-responders by up to about 10%, up to about 20%, up to about 30%, upto about 40%, up to about 50%, up to about 60%, up to about 70%, up toabout 80%, up to about 90% or more.

As used herein, the term “non-responder” refers to an individual forwhich the addition of an anti-SIRPα antibody to a therapy comprisingadministration of a cell-targeting antibody does not significantlyenhance the effectiveness of the cell-targeting antibody. A “responder”is an individual for which the addition of an anti-SIRPα antibody to atherapy comprising administration of a cell-targeting antibodysignificantly enhances the effectiveness of the cell-targeting antibody,and may provide for a synergistic response, in which the level ofactivity is greater than the activity of either antibody as amonotherapy, e.g. when normalized to a negative control.

Suitable anti-SIRPα antibodies include fully human, humanized orchimeric versions of such antibodies, where the Fc region is modified byone or more amino acid changes to reduce FcR binding to one or more Fcother than FcRn. Humanized antibodies are especially useful for in vivoapplications in humans due to their low antigenicity. Similarlycaninized, felinized, etc. antibodies are especially useful forapplications in dogs, cats, and other species respectively. Antibodiesof interest include humanized antibodies, or caninized, felinized,equinized, bovinized, porcinized, etc., antibodies, and variantsthereof.

Variable regions of exemplary antibodies are provided. In someembodiments the variable region comprises the CDR sequences of KWAR23,e.g. as set forth in SEQ ID NO:3, 4, 5 for the heavy chain; and 6, 7, 8for the light chain, joined to a “dead” Fc region or lacking an Fcregion. Antibodies of interest include these provided combinations, aswell as fusions of the variable regions to appropriate constant regionsor fragments of constant regions, e.g. to generate F(ab)' antibodies.Variable regions of interest include at least one CDR sequence of theprovided anti-SIRPα antibody, where a CDR may be 3, 4, 5, 6, 7, 8, 9,10, 11, 12 or more amino acids. Alternatively, antibodies of interestinclude a variable region as set forth in the provided antibodies, orpairs of variable regions sequences as set forth herein.

In other embodiments, a humanized KWAR23 antibody is provided, whichantibody comprises one or both of the variable region sequences providedin SEQ ID NO:1 and SEQ ID NI:2, or a biologically active variant derivedtherefrom. Humanized KWAR23 may comprise a wild-type Fc region, e.g. ahuman Fc region; or may comprise a modified Fc region, e.g. a dead Fc.

Biologically active variants of humanized KWAR23 can include an aminoacid sequence that is 80% or more, 85% or more, 90% or more, 92% ormore, 95% or more, 97% or more, 98% or more, 99% or more, 99.5% or more,or 100% identical to an amino acid sequence set forth in SEQ ID NO:1 orSEQ ID NO:2. In some embodiments the amino acid sequence comprises notmore than 1, not more than 2, not more than 3, not more than 4, not morethan 5, not more than 6, not more than 7, not more than 8, not more than9, not more than 10, etc. amino acid changes relative to the sequence ofSEQ ID NO:1 or SEQ ID NO:2. In some embodiments, amino acid changes arein residues other than CDR residues, as defined, for example, in SEQ IDNO:3, 4, 5, 6, 7, 8, i.e. amino acid changes are in framework sequences.A biologically active variant retains the ability to specifically bindto human SIRPα, usually both the V1 and the V2 variant.

In some embodiments a subject anti-SIRPα antibody includes one more CDRs(e.g., 2 or more, 3 or more, 4 or more, 5 or more, or 6 CDRs) thatincludes an amino acid sequence set forth in SEQ ID NOs: 3-5 and 6-8. Asubject anti-SIRPα antibody can include a CDR sequence that differs byup to 6 amino acids (e.g., up to 5 amino acids, up to 4 amino acids, upto 3 amino acids, up to 2 amino acids, or up to 1 amino acid) ascompared to a CDR amino acid sequence set forth in any of SEQ ID NOs:3-5 and 6-8.

In some cases, a subject anti-SIRPα antibody includes one or more CDRs(e.g., 2 or more, 3 or more, 4 or more, 5 or more, 6, or 6 or more)having an amino acid sequence that differs by up to 6 amino acids (e.g.,up to 5 amino acids, up to 4 amino acids, up to 3 amino acids, up to 2amino acids, or up to 1 amino acid) as compared to a CDR amino acidsequence set forth in any of SEQ ID NOs: 3-5 and 6-8. In some cases, asubject anti-SIRPα antibody includes two or more CDRs (e.g., 3 or more,4 or more, 5 or more, 6, or 6 or more) that have an amino acid sequencethat differs by up to 6 amino acids (e.g., up to 5 amino acids, up to 4amino acids, up to 3 amino acids, up to 2 amino acids, or up to 1 aminoacid) as compared to a CDR amino acid sequence set forth in any of SEQID NOs: 3-5 and 6-8.

In some embodiments, a subject anti-SIRPα antibody includes an aminoacid sequence that is 80% or more, 85% or more, 90% or more, 92% ormore, 95% or more, 97% or more, 98% or more, 99% or more, 99.5% or more,or 100% identical to a CDR amino acid sequence set forth in any of SEQID NOs: 3-5 and 6-8. In some cases, a subject anti-SIRPα antibodyincludes a heavy chain having one or more (e.g., two or more, three ormore, or 3) of the amino acid sequences set forth in SEQ ID NOs: 3-5. Insome cases, a subject anti-SIRPα antibody includes a heavy chain havingall 3 of the amino acid sequences set forth in SEQ ID NOs: 3-5. In somecases, a subject anti-SIRPα antibody includes a light chain having oneor more (e.g., two or more, three or more, or 3) of the amino acidsequences set forth in SEQ ID NOs: 6-8. In some cases, a subjectanti-SIRPα antibody includes a light chain having all 3 of the aminoacid sequences set forth in SEQ ID NOs: 6-8.

In some cases, a subject anti-SIRPα antibody includes a light chainhaving all 3 of the amino acid sequences set forth in SEQ ID NOs: 6-8,and a heavy chain having all 3 of the amino acid sequences set forth inSEQ ID NOs: 3-5.

In some cases, a subject anti-SIRPα antibody includes a heavy chainhaving three CDRs, where CDR-H1 has the amino acid sequence set forth inSEQ ID NO: 3, CDR-H2 has the amino acid sequence set forth in SEQ ID NO:4, and CDR-H3 has the amino acid sequence set forth in SEQ ID NO: 5. Insome cases, a subject anti-SIRPα antibody includes a light chain havingthree CDRs, where CDR-L1 has the amino acid sequence set forth in SEQ IDNO: 6, CDR-L2 has the amino acid sequence set forth in SEQ ID NO: 7, andCDR-L3 has the amino acid sequence set forth in SEQ ID NO: 8. In somecases, a subject anti-SIRPα antibody includes: (i) a heavy chain havingthree CDRs, where CDR-H1 has the amino acid sequence set forth in SEQ IDNO: 3, CDR-H2 has the amino acid sequence set forth in SEQ ID NO: 4, andCDR-H3 has the amino acid sequence set forth in SEQ ID NO:5; and (ii) alight chain having three CDRs, where CDR-L1 has the amino acid sequenceset forth in SEQ ID NO: 6, CDR-L2 has the amino acid sequence set forthin SEQ ID NO: 7, and CDR-L3 has the amino acid sequence set forth in SEQID NO: 8.

In some embodiments, a subject antibody is a bispecific antibody. Theterms “multispecific” or “bispecific” antibodies (also known asbifunctional antibodies or multifunctional antibodies) refer toantibodies that recognize two or more different antigens by virtue ofpossessing at least one region (e.g., derived from a variable region ofa first antibody) that is specific for a first antigen, and at least asecond region (e.g., derived from a variable region of a secondantibody) that is specific for a second antigen. A bispecific antibodyspecifically binds to two target antigens and is thus one type ofmultispecific antibody. Multispecific antibodies can be produced byrecombinant DNA methods or include, but are not limited to, antibodiesproduced chemically by any convenient method. Bispecific antibodiesinclude all antibodies or conjugates of antibodies, or polymeric formsof antibodies which are capable of recognizing two different antigens.Bispecific antibodies include antibodies that have been reduced andreformed so as to retain their bivalent characteristics and toantibodies that have been chemically coupled so that they can haveseveral antigen recognition sites for each antigen.

Subject bispecific antibodies are directed against SIRPα and a secondantigen. Subject bispecific antibodies will allow for the phagocytosisof cellular populations expressing the second antigen. Exemplarybispecific antibodies include those targeting a combination of SIRPα anda cancer cell marker, such as, CD19, CD20, CD22, CD24, CD25, CD30, CD33,CD38, CD44, CD52, CD56, CD70, CD96, CD97, CD99, CD123, CD279 (PD-1),CD274 (PD-L1); EGFR, HER2, CD117, C-Met, PTHR2, HAVCR2 (TIM3), etc. Assuch, in some cases, a subject antibody is a bispecific or multispecificantibody that specifically binds to SIRPα and at least a second antigen.In some such cases, the second antigen is selected from: CD19, CD20,CD22, CD24, CD25, CD30, CD33, CD38, CD44, CD52, CD56, CD70, CD96, CD97,CD99, CD123, CD279 (PD-1), CD274 (PD-L1); EGFR, HER2, CD117, C-Met,PTHR2, HAVCR2 (TIM3).

In some cases, an exemplary bispecific antibody includes a sequence(e.g., CDRs) disclosed herein that provides specific binding to SIRPα aswell as sequences (e.g., CDRs) from antibodies that bind a cancer cellmarker. Examples of antibodies with CDRs that provide specific bindingto a cancer cell marker include, but are not limited to: CETUXIMAB(binds EGFR), PANITUMUMAB (binds EGFR), RITUXIMAB (binds CD20),TRASTUZUMAB (binds HER2), PERTUZUMAB (binds HER2), ALEMTUZUMAB (bindsCD52), BRENTUXIMAB (binds CD30), and the like.

Methods to generate bispecific antibodies are described in theliterature, for example, in U.S. Pat. Nos. 5,989,830, 5,798,229, whichare incorporated herein by reference. Higher order specificities, e.g.trispecific antibodies, are described by Holliger and Hudson (2005)Nature Biotechnology 23:1126-1136.

Within the context of the present disclosure, antibodies are understoodto include monoclonal antibodies and polyclonal antibodies, antibodyfragments (e.g., Fab and F(ab′)₂), chimeric antibodies bifunctional orbispecific antibodies and tetrameric antibody complexes. Antibodies mayalso be described or specified in terms of their binding affinities ofthe variable region for an epitope, i.e. for SIRPα, including thosecharacterized by a K_(d) (dissociation constant) of 10⁻⁵ M or less(e.g., 10⁻⁶ M or less, 10⁻⁷ M or less, 10⁻⁸ M or less, 10⁻⁹ M or less,10⁻¹⁰ M or less, 10⁻¹¹ M or less, 10⁻¹² M or less, 10⁻¹³ M or less,10⁻¹⁴ M or less, 10⁻¹⁵ M or less, or 10⁻¹⁶ M or less). For bispecificand/or multispecific antibodies, which have more than one specificity(i.e., more than 1 binding constant), each antigen-specific region canhave a K_(d) (dissociation constant) of 10⁻⁵ M or less (e.g., 10⁻⁶ M orless, 10⁻⁷ M or less, 10⁻⁸ M or less, 10⁻⁹ M or less, 10⁻¹⁰ M or less,10⁻¹¹ M or less, 10⁻¹² M or less, 10⁻¹³ M or less, 10⁻¹⁴ M or less,10⁻¹⁵ M or less, or 10⁻¹⁶ M or less).

Antibodies may be characterized by reduced binding to one or more FcRother than FcRn, where the binding to one or more FcR, including withoutlimitation or more FcγR is reduced by at least about 10%, at least about20%, at least about 30%, at least about 40%, at least about 50%, atleast about 60%, at least about 70%, at least about 80%, at least about90%, at least about 95%, at least about 99%, or more.

Nucleic Acids

The disclosure also provides isolated nucleic acids encoding subjectanti-SIRPα antibodies (e.g., including any of the polypeptides discussedabove), vectors and host cells comprising the nucleic acid, andrecombinant techniques for the production of the antibody. As is knownin the art, a variable region sequence may be fused to any appropriateconstant region sequence.

For recombinant production of the antibody, the nucleic acid encodingcan be inserted into a replicable vector for further cloning(amplification of the DNA) or for expression. DNA encoding a subjectantibody can be readily isolated and sequenced using conventionalprocedures (e.g., by using oligonucleotide probes that are capable ofbinding specifically to genes encoding the heavy and light chains of theantibody). Many vectors are available. The vector components generallyinclude, but are not limited to, one or more of the following: a signalsequence, an origin of replication, one or more marker genes, anenhancer element, a promoter, and a transcription termination sequence.

A subject anti-SIRPα antibody of this disclosure may be producedrecombinantly not only directly, but also as a fusion polypeptide with aheterologous or homologous polypeptide, which include a signal sequenceor other polypeptide having a specific cleavage site at the N-terminusof the mature protein or polypeptide, an immunoglobulin constant regionsequence, and the like. A heterologous signal sequence selectedpreferably may be one that is recognized and processed (i.e., cleaved bya signal peptidase) by the host cell. For prokaryotic host cells that donot recognize and process the native antibody signal sequence, thesignal sequence is substituted by a prokaryotic signal sequenceselected.

An “isolated” nucleic acid molecule is a nucleic acid molecule that isidentified and separated from at least one contaminant nucleic acidmolecule with which it is ordinarily associated in the natural source ofthe antibody nucleic acid. An isolated nucleic acid molecule is otherthan in the form or setting in which it is found in nature. Isolatednucleic acid molecules therefore are distinguished from the nucleic acidmolecule as it exists in natural cells. However, an isolated nucleicacid molecule includes a nucleic acid molecule contained in cells thatordinarily express the antibody where, for example, the nucleic acidmolecule is in a chromosomal location different from that of naturalcells.

Examples of suitable host cells for cloning or expressing subjectnucleic acids include, but are not necessary limited to prokaryote,yeast, or higher eukaryote cells. Examples of useful mammalian host celllines are monkey kidney CV1 line transformed by SV40 (COS-7, ATCC CRL1651); human embryonic kidney line (293 or 293 cells subcloned forgrowth in suspension culture, Graham et al., J. Gen Virol. 36:59(1977)); baby hamster kidney cells (BHK, ATCC CCL 10); Chinese hamsterovary cells/-DHFR(CHO, Urlaub et al., Proc. Natl. Acad. Sci. USA 77:4216(1980)); mouse sertoli cells (TM4, Mather, Biol. Reprod. 23:243-251(1980)); monkey kidney cells (CV1 ATCC CCL 70); African green monkeykidney cells (VERO-76, ATCC CRL-1587); human cervical carcinoma cells(HELA, ATCC CCL 2); canine kidney cells (MDCK, ATCC CCL 34); buffalo ratliver cells (BRL 3A, ATCC CRL 1442); human lung cells (W138, ATCC CCL75); human liver cells (Hep G2, HB 8065); mouse mammary tumor (MMT060562, ATCC CCL51); TR1 cells (Mather et al., Annals N.Y. Acad. Sci.383:44-68 (1.982)); MRC 5 cells; FS4 cells; and a human hepatoma line(Hep G2). Host cells are transformed with the above-described expressionor cloning vectors for anti-SIRPα antibody production and cultured inconventional nutrient media modified as appropriate for inducingpromoters, selecting transformants, or amplifying the genes encoding thedesired sequences.

The antibody composition prepared from the cells can be purified using,for example, hydroxylapatite chromatography, gel electrophoresis,dialysis, and affinity chromatography, with affinity chromatographybeing the preferred purification technique. The suitability of protein Aas an affinity ligand depends on the species and isotype of anyimmunoglobulin Fc domain that is present in the antibody. Protein A canbe used to purify antibodies that are based on human γ1, γ2, or γ4 heavychains (Lindmark et al., J. Immunol. Meth. 62:1-13 (1983)). Protein G isusually recommended for human IgG3 (Guss et al., EMBO J. 5:15671575(1986)). The matrix to which the affinity ligand is attached is mostoften agarose, but other matrices are available. Mechanically stablematrices such as controlled pore glass or poly(styrenedivinyl)benzeneallow for faster flow rates and shorter processing times than can beachieved with agarose. Where the antibody comprises a CH₃ domain, theBakerbond ABX™ resin (J. T. Baker, Phillipsburg, N.J.) is useful forpurification. Other techniques for protein purification such asfractionation on an ion-exchange column, ethanol precipitation, ReversePhase HPLC, chromatography on silica, chromatography on heparinSEPHAROSE™ chromatography on an anion or cation exchange resin (such asa polyaspartic acid column), chromatofocusing, SDS-PAGE, and ammoniumsulfate precipitation are also available depending on the antibody to berecovered.

Following any preliminary purification step(s), the mixture comprisingthe antibody of interest and contaminants may be subjected to low pHhydrophobic interaction chromatography using an elution buffer at a pHbetween about 2.5-4.5, preferably performed at low salt concentrations(e.g., from about 0-0.25M salt).

Methods of Use

The anti-SIRPα antibodies provided herein can be used in the modulationof phagocytosis (e.g. inducing phagocytosis), particularly for in vivotherapeutic uses. For example, the subject anti-SIRPα antibodiesprovided herein can be used, in any method where the interaction betweenCD47 on one cell and SIRPα on another is to be blocked. Exemplarymethods for using a subject anti-SIRPα antibody include, but are notlimited to those methods described in U.S. patent applications:20130142786, 20120282174, 20110076683, 20120225073, 20110076683,20110015090, 20110014119, 20100239579, 20090191202, 20070238127,20070111238, and 20040018531; which are hereby specifically incorporatedby reference in their entirety. For example, antibody compositions maybe administered to induce phagocytosis of cancer cells, inflammatorycells, and/or chronically infected cells that express CD47.

A subject anti-SIRPα antibody provided herein may administered, alone orin combination with another antibody to a subject to treat symptoms,illnesses, and/or diseases. Examples of symptoms, illnesses, and/ordiseases that can be treated with a subject anti-SIRPα antibody include,but are not limited to cancer (any form of cancer, including but notlimited to: carcinomas, soft tissue tumors, sarcomas, teratomas,melanomas, leukemias, lymphomas, brain cancers, solid tumors,mesothelioma (MSTO), etc.); infection (e.g., chronic infection);cardiovascular conditions, e.g. atherosclerosis, aneurysm, etc., andimmunological diseases or disorders (e.g., an inflammatorydisease)(e.g., multiple sclerosis, arthritis, and the like)(e.g., forimmunosuppressive therapy). A subject anti-SIRPα antibody can also beused for transplant conditioning (e.g., stem cell transplant, bonemarrow transplant, etc.) (e.g., to destroy malignant cells, to provideimmunosuppression to prevent the patient's body from rejecting thedonor's cells/stem cells, etc.)

In some embodiments, a subject anti-SIRPα antibody (including, forexample, a bispecific macrophage engaging antibody) is used incombination with another antibody to treat an individual. In oneembodiment, a subject anti-SIRPα antibody can be combined(co-administered) with monoclonal antibodies directed against one ormore cancer markers (e.g., CD19, CD20, CD22, CD24, CD25, CD30, CD33,CD38, CD44, CD52, CD56, CD70, CD96, CD97, CD99, CD123, CD279 (PD-1),CD274 (PD-L1); EGFR, HER2, CD117, C-Met, PTHR2, HAVCR2 (TIM3), and thelike). In some cases, the combination compositions can be synergistic inenhancing phagocytosis of target cells as compared to the use of singleantibodies. As proof of principle, CD47-directed agents (e.g., anti-CD47antibodies) exhibit profound anti-tumor synergy with monoclonalantibodies (mAbs) against tumor-specific antigens, such as rituximab(anti-CD20) for B-cell lymphoma and trastuzumab (anti-HER2) for HER2+breast cancer. The Fc fragments of these mAbs activate Fc receptors(FcRs) on macrophages to drive a phosphorylation cascade propagated bythe receptors' ITAMs (Immunoreceptor Tyrosine-based Activation Motifs).As SIRPα signals through counter-opposing ITIMs (ImmunoreceptorTyrosine-based Inhibitory Motifs), blocking SIRPα tips the balance infavor of ITAM signaling, thereby potentiating phagocytosis.

In some embodiments, a subject anti-SIRPα antibody is co-administeredwith (i.e., administered in combination with) an antibody thatspecifically binds a second antigen, e.g., a marker of a CD47-expressingcell (e.g., a cancer cell marker, a marker of an infected cell, etc.),including without limitation tumor associated and tumor specificantigens. For example, in some cases, a subject anti-SIRPα antibody isco-administered with 1 or more antibodies selected from: CETUXIMAB(binds EGFR), PANITUMUMAB (binds EGFR), RITUXIMAB (binds CD20),TRASTUZUMAB (binds HER2), PERTUZUMAB (binds HER2), ALEMTUZUMAB (bindsCD52), and BRENTUXIMAB (binds CD30) , GEMTUZUMAB (binds CD33),LORVOTUZUMAB (binds CD56), IPILIMUMAB (binds CTLA-4 (CD152)), NIVOLUMAB(binds PD-1 (CD279), AVELUMAB (binds PDL-1), etc.

Therapeutic formulations comprising one or more antibodies of thedisclosure are prepared for storage by mixing the antibody having thedesired degree of purity with optional physiologically acceptablecarriers, excipients or stabilizers (Remington's Pharmaceutical Sciences16th edition, Osol, A. Ed. (1980)), in the form of lyophilizedformulations or aqueous solutions. The antibody composition will beformulated, dosed, and administered in a fashion consistent with goodmedical practice. Factors for consideration in this context include theparticular disorder being treated, the particular mammal being treated,the clinical condition of the individual patient, the cause of thedisorder, the site of delivery of the agent, the method ofadministration, the scheduling of administration, and other factorsknown to medical practitioners. The “therapeutically effective amount”of the antibody to be administered will be governed by suchconsiderations, and is the minimum amount necessary to prevent the CD47associated disease.

The therapeutic dose may be at least 0.01 mg/kg body weight, at least0.05 mg/kg body weight; at least 0.1 mg/kg body weight, at least 0.5mg/kg body weight, at least 1 mg/kg body weight, at least 2.5 mg/kg bodyweight, at least 5 mg/kg body weight, at least about 7.5 mg/kg bodyweight, at least about 10 mg/kg body weight, at least about 15 mg/kgbody weight, and not more than 300 mg/kg body weight, not more thanabout 200 mg/kg body weight, not more than about 100 mg/kg body weight.It will be understood by one of skill in the art that such guidelineswill be adjusted for the molecular weight of the active agent, e.g. inthe use of antibody fragments, or in the use of antibody conjugates. Thedosage may also be varied for localized administration, e.g. intranasal,inhalation, etc., or for systemic administration, e.g. i.m., i.p., i.v.,and the like.

The antibody need not be, but is optionally formulated with one or moreagents that potentiate activity, or that otherwise increase thetherapeutic effect. These are generally used in the same dosages andwith administration routes as used hereinbefore or about from 1 to 99%of the heretofore employed dosages.

Acceptable carriers, excipients, or stabilizers are non-toxic torecipients at the dosages and concentrations employed, and includebuffers such as phosphate, citrate, and other organic acids;antioxidants including ascorbic acid and methionine; preservatives (suchas octadecyidimethylbenzyl ammonium chloride; hexamethonium chloride;benzalkonium chloride, benzethonium chloride; phenol, butyl or benzylalcohol; alkyl parabens such as methyl or propyl paraben; catechol;resorcinol; cyclohexanol; 3-pentanol; and m-cresol); low molecularweight (less than 10 residues) polypeptides; proteins, such as serumalbumin, gelatin, or immunoglobulins; hydrophilic polymers such aspolyvinylpyrrolidone; amino acids such as glycine, glutamine,asparagine, histidine, arginine, or lysine; monosaccharides,disaccharides, and other carbohydrates including glucose, mannose, ordextrins; chelating agents such as EDTA; sugars such as sucrose,mannitol, trehalose or sorbitol; salt-forming counter-ions such assodium; metal complexes (e.g., Zn-protein complexes); and/or non-ionicsurfactants such as TWEEN™, PLURONICS™ or polyethylene glycol (PEG).Formulations to be used for in vivo administration must be sterile. Thisis readily accomplished by filtration through sterile filtrationmembranes.

The active ingredients may also be entrapped in microcapsule prepared,for example, by coacervation techniques or by interfacialpolymerization, for example, hydroxymethylcellulose orgelatin-microcapsule and poly-(methylmethacylate) microcapsule,respectively, in colloidal drug delivery systems (for example,liposomes, albumin microspheres, microemulsions, nano-particles andnanocapsules) or in macroemulsions. Such techniques are disclosed inRemington's Pharmaceutical Sciences 16th edition, Osol, A. Ed. (1980).

The anti-SIRPα antibody is administered by any suitable means, includingparenteral, subcutaneous, intraperitoneal, intrapulmonary, andintranasal. Parenteral infusions include intramuscular, intravenous,intraarterial, intraperitoneal, or subcutaneous administration. Inaddition, the anti-SIRPα antibody is suitably administered by pulseinfusion, particularly with declining doses of the antibody.

For the prevention or treatment of disease, the appropriate dosage ofantibody will depend on the type of disease to be treated, as definedabove, the severity and course of the disease, whether the antibody isadministered for preventive purposes, previous therapy, the patient'sclinical history and response to the antibody, and the discretion of theattending physician. The antibody is suitably administered to thepatient at one time or over a series of treatments.

In another embodiment of the disclosure, an article of manufacturecontaining materials useful for the treatment of the disorders describedabove is provided. The article of manufacture comprises a container anda label. Suitable containers include, for example, bottles, vials,syringes, and test tubes. The containers may be formed from a variety ofmaterials such as glass or plastic. The container holds a compositionwhich is effective for treating the condition and may have a sterileaccess port (for example the container may be an intravenous solutionbag or a vial having a stopper pierceable by a hypodermic injectionneedle). An active agent in the composition can be the anti-SIRPαantibody. The label on, or associated with, the container can indicatethat the composition is used for treating the condition of choice. Thearticle of manufacture may further comprise a second containercomprising a pharmaceutically-acceptable buffer, such asphosphate-buffered saline, Ringer's solution and dextrose solution. Itmay further include other materials desirable from a commercial and userstandpoint, including other buffers, diluents, filters, needles,syringes, and package inserts with instructions for use.

A subject anti-SIRPα antibody of the present disclosure can be providedin a kit, i.e., a packaged combination of reagents in predeterminedamounts with instructions for administration and/or for performing anassay. In some cases, a subject kit can include one or more additionalantibodies that can be used in combination with an anti-SIRPα antibody.For example, in some cases, a subject kit includes one or moreantibodies that each binds a second antigen (e.g., a cancer cellmarker). In some embodiments, the second antigen is an antigen selectedfrom: CD19, CD20, CD22, CD24, CD25, CD30, CD33, CD38, CD44, CD52, CD56,CD70, CD96, CD97, CD99, CD123, CD279 (PD-1), CD274 (PD-L1); EGFR, HER2,CD117, C-Met, PTHR2, and HAVCR2 (TIM3). In some embodiments, a subjectkit includes a subject SIRPα antibody and one or more antibodiesselected from: CETUXIMAB (binds EGFR), PANITUMUMAB (binds EGFR),RITUXIMAB (binds CD20), TRASTUZUMAB (binds HER2), PERTUZUMAB (bindsHER2), ALEMTUZUMAB (binds CD52), and BRENTUXIMAB (binds CD30),GEMTUZUMAB (binds CD33), LORVOTUZUMAB (binds CD56), IPILIMUMAB (bindsCTLA-4 (CD152)), and NIVOLUMAB (binds PD-1 (CD279)).

When the antibody is labeled with an enzyme, the kit can includesubstrates and cofactors required by the enzyme (e.g., a substrateprecursor which provides the detectable chromophore or fluorophore). Inaddition, other additives may be included such as stabilizers, buffers(e.g., a block buffer or lysis buffer) and the like. The relativeamounts of the various reagents may be varied widely to provide forconcentrations in solution of the reagents which substantially optimizethe sensitivity of the assay. Particularly, the reagents may be providedas dry powders, usually lyophilized, including excipients which ondissolution will provide a reagent solution having the appropriateconcentration.

The invention now being fully described, it will be apparent to one ofordinary skill in the art that various changes and modifications can bemade without departing from the spirit or scope of the invention.

EXPERIMENTAL

The following examples are put forth so as to provide those of ordinaryskill in the art with a complete disclosure and description of how tomake and use the present invention, and are not intended to limit thescope of what the inventors regard as their invention nor are theyintended to represent that the experiments below are all or the onlyexperiments performed. Efforts have been made to ensure accuracy withrespect to numbers used (e.g. amounts, temperature, etc.) but someexperimental errors and deviations should be accounted for. Unlessindicated otherwise, parts are parts by weight, molecular weight isweight average molecular weight, temperature is in degrees Centigrade,and pressure is at or near atmospheric.

All publications and patent applications cited in this specification areherein incorporated by reference as if each individual publication orpatent application were specifically and individually indicated to beincorporated by reference.

The present invention has been described in terms of particularembodiments found or proposed by the present inventor to comprisepreferred modes for the practice of the invention. It will beappreciated by those of skill in the art that, in light of the presentdisclosure, numerous modifications and changes can be made in theparticular embodiments exemplified without departing from the intendedscope of the invention. For example, due to codon redundancy, changescan be made in the underlying DNA sequence without affecting the proteinsequence. Moreover, due to biological functional equivalencyconsiderations, changes can be made in protein structure withoutaffecting the biological action in kind or amount. All suchmodifications are intended to be included within the scope of theappended claims.

Example 1

Blocking the CD47-SIRPα pathway mediates phagocytosis of cancer cellsand synergizes with cancer-targeting monoclonal antibodies. Blockingagents include, for example, antibodies that specifically bind to CD47,and antibodies that specifically bind to SIRPα. The latter may havecertain advantages in therapeutic applications because expression ofSIRPα is more restricted than CD47. This may impact pharmacokinetics andthe toxicology profile.

Following administration to a patient, a desirable agent will retainbiological activity for a period of time sufficient to effect atherapeutic benefit. For example, in the treatment of cancer and otherchronic conditions, a half like of days to weeks may be preferred.Antibodies comprising an Fc region can readily achieve this level ofstability, which is thought to be mediated, at least in part, byinteraction of the Fc region with the low affinity receptor, hFcRn,which is involved in recycling and transport of IgG.

Another desirable attribute of therapeutic agents is minimalimmunogenicity when administered to a patient. For this reason,antibodies for human therapy are typically modified to comprise at leasta human Fc region (in the case of chimeric antibodies); or humanframework and constant regions (in the case of humanized antibodies).The therapeutic use of antibodies that have a xenogeneic Fc region isgenerally counter-indicated.

It is important to note that for various purposes, in vitro modelsystems, or engineered in vivo animal models, may be used to determinethe toxicity and efficacy of an agent. In such model systems, there maybe a “mismatch” of the target cells and the effector cells that arepresent, e.g. where human cancer cells are xenografted into a mouse.While useful for many purposes, such models may not accurately predictthe activity of activity of an antibody in a patient setting, where thetarget cells and the effector cells will be of the same species, e.g.human. For these reasons, advantageous information about therapeuticefficacy is obtained by testing the activity of a human or humanizedantibody against human target cells, in the presence of human effectorcells.

Native human antibodies are glycoproteins that contain a ubiquitousN-linked glycan at position N297 of the Fc domain (Eu numbering).Studies have demonstrated that altering glycosylation at N297 can modifyinteractions with FcγRs and thereby affect antibody effector functions.The absence of the glycan at N297 abolishes binding to FcγRs andantibody effector functions. Other amino acid changes in Fc regionsinclude the double substitution, L234A/L235A (LALA), which greatlyreduces binding to FcγRs. Aglycosylated antibodies produced in E. colialso have minimal binding to FcγRs and can provide a simplified and moreeconomical antibody production platform.

In preparing anti-SIRPα antibodies for therapeutic purposes, the KWAR23antibody (disclosed in International Application WO 2015/138600, hereinspecifically incorporated by reference) was modified to comprise a humanFc region. Surprisingly it was found that the change in Fc region wasdetrimental to activity in enhancing phagocytosis when combined withcancer targeting monoclonal antibodies in a human effector cell setting.

It was hypothesized that simultaneous engagement of SIRPα and highaffinity Fcγ receptors present on effector cells resulted in inhibitionof phagocytosis, e.g. through formation of a trimolecular complexbetween the antibody, Fcγ receptor, and SIRPα on the cell surface. Toaddress the issue, Fcγ receptor engagement was blocked by replacing theFc of the anti-SIRPα antibody with a so-called “dead Fc”, i.e. an Fcregion engineered to have reduced binding to Fcγ receptors by theintroduction of amino acid changes. The specific engineered Fc regioncomprised an N297A amino acid substitution in the human IgG1 constantregion. As shown in FIG. 1 , this modification did overcome theinhibitory effect and restored the desired phagocytosis promotingeffect.

Example 2

Anti-SIRPα antibodies with reduced FcγR binding for phagocytosis of NHLcells by human macrophages in combination with rituximab in vitro.Anti-human SIRPα antibodies comprising an engineered Fc region, asdiscussed in Example 1, are assessed for the ability to enablephagocytosis of human NHL cell lines, primary NHL cells, and normalperipheral blood (NPB) cells by human macrophages in vitro. NHL cellsare incubated in the presence of IgG1 isotype control or anti-CD45 IgG1antibody, and compared to the activity in the presence of a humanizedanti-SIRPα antibody with a wild-type or engineered N297A Fc region, inthe presence of rituximab. The phagocytosis of the tumor cells underthese conditions is measured.

Cell Lines. A Burkitt's lymphoma cell line (Raji) and a DLBCL cell line(SUDHL4) are obtained from the American Type Culture Collection orgenerated in the lab. The NHL17* cell line is generated from a patientwith DLBCL by culturing bulk cells in vitro with IMDM supplemented with10% human AB serum for 1.5 months.

Human Samples. Normal human peripheral blood and human NHL samples areobtained with informed consent, according to an IRB-approved protocol orwith informed consent from the Norwegian Radium Hospital (Oslo, Norway)according to a Regional Ethic Committee (REK)-approved protocol. Normaltonsils for germinal center B cell analysis are obtained from discardedtonsillectomy specimens from consented pediatric patients.

Flow Cytometry Analysis. For analysis of normal peripheral blood cells,germinal center B cells, and primary NHL cells, the following antibodieswere used: CD19, CD20, CD3, CD10, CD45, CD5, CD38 (Invitrogen, Carlsbad,Calif., USA and BD Biosciences, San Jose, Calif., USA). Analysis of CD47expression is performed with an antihuman CD47 FITC antibody (cloneB6H12.2, BD Biosciences). Cell staining and flow cytometry analysis wasperformed as previously described.

Therapeutic Antibodies. Rituximab (anti-CD20, human IgG1) is obtainedfrom the Stanford University Medical Center, mouse anti-human CD20,IgG2a from Beckman Coulter (Miami, Fla., USA).

In Vitro lsobologram Studies. In vitro phagocytosis assays are conductedwith NHL cells incubated with the indicated antibodies, anti-CD20 IgG2a,or rituximab either alone or in combination at concentrations from 1μg/ml to 10 μg/ml. The concentration of each antibody required toproduce a defined single-agent effect (phagocytic index) is determinedfor each cell type. Concentrations of the two antibodies combined toachieve this same phagocytic index were then plotted on an isobologramand the combination index (CI) determined. The CI is calculated from theformula CI=(d1/D1)+(d2/D2), whereby d1=dose of drug 1 in combination toachieve the phagocytic index, d2=dose of drug 2 in combination toachieve the phagocytic index, D1=dose of drug 1 alone to achieve thephagocytic index, D2=dose of drug 2 alone to achieve the phagocyticindex. A CI of less than, equal to, and greater than 1 indicatessynergy, additivity, and antagonism, respectively.

Example 3

Anti-SIRPα antibodies with reduced FcγR binding for phagocytosis ofcolorectal cancer cells by human macrophages in combination withanti-EGFR in vitro. Cancer Cells. DLD1 cells (ATCC), HT29 cells (ATCC),SW620 cells (ATCC), SW48 cells (ATCC), LS174T cells (ATCC), HCT116 cells(ATCC), and CACO-2 cells (ATCC) are cultured in RPMI (ThermoFisher S.)(DLD1), EMEM (ThermoFisher S.) (CACO-2, LS174T), McCoy's 5A(ThermoFisher S.) (HT29, HCT116), or Leibovitz's L-15 (ThermoFisher S.)(SW48, SW 620) supplemented with 10% fetal bovine serum (OmegaScientific), 100 U/mL penicillin and 100 μg/mL streptomycin(ThermoFisher S). GFP-luciferase+DLD1 cell line was generated bytransduction using a pCDH-CMV-MCS-EF1 puro HIV-based lentiviral vector(Systems Biosciences) engineered to express an eGFP-luciferase2 (pgl4)fusion protein. Stable lines were created by sorting for GFP expressionon FACSAria II cell sorters (BD Biosciences). Tumor cells weretransduced overnight with lentivirus in culture media containing 6 μg/mLpolybrene. The following day, cells were washed repeatedly to removepolybrene and extracellular lentivirus. Transduced (GFP+) cells werelater isolated from xenograft tumors by FACS.

In Vitro Phagocytosis Assay. Peripheral blood mononuclear cells areenriched by density gradient centrifugation and monocytes purified withanti-CD14 microbeads (Miltenyi) and differentiated to macrophages byculture for 7-10 days in IMDM+GlutaMax (Invitrogen) supplemented with10% AB-Human Serum (Invitrogen) and 100 U/mL penicillin and 100 μg/mLstreptomycin (Invitrogen). Phagocytosis assays are performed byco-culture of 50,000 macrophages with 100,000 GFP+ tumor cells for 2hours, then analyzed using an LSRFortessa cell analyzer with highthroughput sampler (BD Biosciences). Antibodies used for treatmentinclude: IgG1 isotype control, anti-SIRPα with an active or dead Fcregion, and anti-EGFR cetuximab (Bristoll-Myers Squibb). Macrophages areidentified by flow cytometry using anti-CD206 antibody. Dead cells wereexcluded from the analysis by staining with DAPI (Sigma). Phagocytosisis evaluated as the percentage of GFP+ macrophages and normalized to themaximal response by each independent donor against each cell line.

Example 4 Avelumab in Combination With Anti-SIRPα in AdvancedMalignancies

Using the assays described above, the combination of anti-SIRPα antibodywith a wild-type or dead Fc is tested for phagocytosis and/or cellmediated cytolysis in vitro of advanced or metastatic solid tumors [eg,non-small cell lung cancer (NSCLC), melanoma, and squamous cellcarcinoma of the head and neck (SCCHN)] in combination with avelumab(MSB0010718C), an anti-PD-L1 antibody.

Example 5 Variability in Individual Responses

Antibodies were generated with anti-SIRPα KWAR23 variable region with amouse Fc sequence (designated mKWAR); a chimeric with a human Fcsequence comprising N297A mutation to abrogate interaction with humanFcγRs (designated chKWAR-dead-Fc); a chimeric with a wild-type humanIgG1 Fc (designated chKWAR-IgG1); and a chimeric with human IgG4 Fcregion, (designated chKWAR-IgG4).

The antibodies were assayed for a synergistic response in enhancingphagocytosis of cancer cells, when combined with rituximab, data shownin FIG. 2 .

Human macrophages from 10 different donors were differentiated frommonocytes, as indicated by DONOR #, in the presence of human serum for 7days. Raji lymphoma cells were labeled with CFSE (Carboxyfluoresceinsuccinimidyl ester is a fluorescent cell staining dye) and incubatedwith the macrophages in the presence of 10 μg/ml rituximab (anti-CD20Ab) alone, in combination with 10 μg/ml of the KWAR variants or humanIgG4 as control. After two-hour incubation, phagocytosis was determinedby flow cytometry analysis as CFSE-positive macrophages. Baselinephagocytosis was determined with the human IgG4 control Ab. Combinationof rituximab with human IgG control Ab was used to establish rituximabspecific baseline phagocytosis The dotted line indicates the level ofphagocytosis with rituximab alone.

In testing responses from multiple individuals, it was found that therewas inter-individual variability in the enhancement of phagocytosis. Thecombination of rituximab with murine anti-SIRPα Ab (mKWAR) enhancedphagocytosis for all ten donor macrophages compared to rituximab alone(indicated as increase above dotted line).

In contrast, the combination of rituximab with chimeric anti-SIRPα Ab(chKWAR-IgG4) showed a significant enhancement of phagocytosis for donormacrophages for three donors, but not for the other seven donors.Similarly, in the 6 donors tested with a wild-type IgG1 Fc region(chKWAR-IgG1) half of the donors showed no significant enhancement overcontrol.

In contrast, all ten donors had a significant enhancement ofphagocytosis when the chimeric anti-SIRPα Ab with a “dead” IgG1-Fcregion (KWAR-dead-Fc) was combined with rituximab.

These experiments demonstrate the general benefit of the dead-Fcconstruct for anti-SIRPα antibodies, in reducing variability ofresponsiveness, i.e. reducing the number of individuals that arenon-responders in the enhancement of phagocytosis when combined with acell-targeted antibody.

Example 6 Additional Anti-SIRPα Antibodies

Additional antibodies were raised to human SIRPα by immunizing mice withthe human protein, and screening for antibodies that bound to the SIRPα.Two monoclonal antibody clones were designated 9B11 and 7E11,respectively. The mouse variable regions were joined as a chimera tohuman IgG4 Fc region (designated as 7E11-G4 or 9B11-G4), or to a humanIgG1 Fc region comprising N297A mutation to abrogate interaction withhuman FcγRs (designated as 7E11-G1 or 9B11-G1).

As was found with KWAR23, the 9B11 and 7E11 antibodies showed asynergistic response in enhancing phagocytosis of cancer cells whencombined with Rituximab. Shown in FIG. 3 , macrophages weredifferentiated from monocytes of donor A (A) and donor B (B) in thepresence of human serum for 7 days. Raji cells were labeled with CFSEand incubated with the macrophages in the presence of 10 μg/ml rituximab(Rx) alone or in combination with 10 μg/ml of 9B11-G4, 9B11-G1, 7E11-G4,or 7E11-G1. Two hours later, Phagocytosis percentage was calculated byFlow Cytometry analysis looking for GFP+ Macrophages.

The data show that while both the IgG4 formatted antibodies and mutatedIgG1 formatted antibodies could provide for a synergistic response, butthe mutated IgG1 format provided a more consistent response acrossdonors.

Example 7 F(ab)2 Fragments

As an alternative to the use of an antibody comprising a human Fc regionwith reduced affinity for an Fcγ receptor, an antibody can be engineeredto lack Fc sequences, e.g. by producing an F(ab′)2 fragment.

The anti-SIRPα antibody KWAR23, disclosed, for example in US patentapplication US-2017-0073414-A1, herein specifically incorporated byreference was originally developed as a mouse anti-human antibody. Togenerate an F(ab)2 fragment, the purified antibody is suspended withPierce F(ab′)2 Preparation pepsin immobilized on settled resin,according to the manufacturer's instructions. Pepsin digestion typicallyproduces a F(ab′)2 fragment (˜110 kDa by SDS-PAGE under non-reducingconditions) and numerous small peptides of the Fc portion. The resultingF(ab′)2 fragment is composed of a pair of Fab′ units connected by twodisulfide bonds. The Fc fragment is extensively degraded and separatedfrom F(ab′)2 by dialysis, gel filtration or ion exchange chromatography.

Example 8 Humanized KWAR Antibody

The anti-SIRPα antibody KWAR23, disclosed, for example in US patentapplication US-2017-0073414-A1, herein specifically incorporated byreference was originally developed as a mouse anti-human antibody.

Mouse KWAR23 variable heavy chain (VH) (CDRs are underlined)

(SEQ ID NO: 9) EVQLQQSGAELVKPGASVKLSCTASGFNIKDYYIHWVQQRTEQGLEWIGRIDPEDGETKYAPKFQDKATITADTSSNTAYLHLSSLTSEDTAVYYCARWG AYWGQGTLVTVSS

Mouse KWAR23 variable light chain (VL) (CDRs are underlined)

(SEQ ID NO: 10) QIVLTQSPAIMSASPGEKVTLTCSASSSVSSSYLYWYQQKPGSSPKLWIYSTSNLASGVPARFSGSGSGTSYSLTISSMEAEDAASYFCHQWSSYPRTFG AGTKLELK

Humanized KWAR23 variable heavy chain (VH), SEQ ID NO:1:

EVQLVQSGAEVKKPGATVKISCKVSGFNIKDYYIHWVQQAPGKGLEWIGRIDPEDGETKYAPKFQDRATITADTSTDTAYMELSSLRSEDTAVYYCARWG AYWGQGTLVTVSS

Humanized KWAR23 variable light chain (VL), SEQ ID NO:2:

QIVLTQSPPTLSLSPGERVTLTCSASSSVSSSYLYWYQQKPGQAPKLWIYSTSNLASGVPARFSGSGSGTSYTLTISSLQPEDFAVYFCHQWSSYPRTFG AGTKLEIK

The CDRs of KWAR23 variable heavy chain (defined by IMGT) are asfollows:

CDR-H1: (SEQ ID NO: 3) DYYIH CDR-H2: (SEQ ID NO: 4) RIDPEDGETKYAPKFQDCDR-H3: (SEQ ID NO: 5) WGAY

The CDRs of KWAR23 variable light chain (defined by IMGT) are asfollows:

CDR-L1: (SEQ ID NO: 6) SASSSVSSSYLY CDR-L2: (SEQ ID NO: 7) STSNLASCDR-L3: (SEQ ID NO: 8) HQWSSYPRT

In order to select human antibody frameworks (FR) to be used astemplates for CDR-grafting, mouse KWAR23 VL and VH regions were comparedwith those of human germline sequences. Human framework sequences wereselected based on the mouse framework sequences. The FRs from humanselected sequences provided the starting point for designing humanizedKWAR23. Residues in the FRs identical to the mouse sequences wereretained and non-identical residues were either retained or substitutedbased on molecular modeling. The humanized KWAR23 coding sequences weretransfected into cells, and purified. The sequences are shown in FIG. 4.

Next, the ability of humanized KWAR23 to recognize human SIRPα wasexamined by Biacore assay. The binding affinity of the mouse antibodywas determined to be 1.18×10⁻⁹ M. The binding affinity of the humanizedantibody was determined to be 1.54×10⁻⁹ M.

Humanized Kwar was tested for synergy with therapeutic antibodies topromote phagocytosis, shown in FIG. 5 . (A) Raji cells were labeled withCFSE and incubated with human monocyte derived macrophages in thepresence of 10 μg/ml rituximab alone or in combination with 10 μg/ml ofHuKwar-G1. Data presented was results from 6 individual donors. (B) HT29cells were labeled with CFSE and incubated with human monocyte derivedmacrophages in the presence of 0.1 ug/ml cetuximab alone or incombination with 10 ug/ml of HuKWar-G1. Two hours later, Phagocytosispercentage was calculated by Flow Cytometry analysis looking for GFP+Macrophages. Data presented was results from 6 individual donors. HumanIgG1 is engineered to have a N297A mutation to abrogate the interactionwith human FcγRs. The data show a synergy of response for the humanizedantibody with both tumor-specific antibodies.

In summary, we have developed therapeutic antibodies based on the mousemonoclonal antibody KWAR23 directed against human SIRPα, by usingmethods to create a mouse/human chimeric antibody and a humanizedantibody. The chimeric and humanized antibodies retain the ability tospecifically bind SIRPα.

That which is claimed is:
 1. An isolated, therapeutic antibodycomprising: (i) a variable region that specifically binds to humanSIRPα, comprising a light chain having all three of amino acid sequencesset forth in SEQ ID NOs: 6-8, and a heavy chain having all three aminoacid sequences set forth in SEQ ID NOs: 3-5; (ii) a human Fc regioncomprising an amino acid substitution (a) in the CH2 region at EU indexpositions 234, 235, or 237; or (b) at EU index position asparagine 297,which amino acid substitution reduces binding to a human Fcγ receptor,relative to a wild-type Fc region.
 2. The antibody of claim 1,comprising an amino acid substitution of N297A/Q/D/H/G/C.
 3. Theantibody of claim 1, wherein the amino acid substitution is L234A/L235A.4. The antibody of claim 2, further comprising the amino acidsubstitution K322A.
 5. The antibody of claim 1, wherein the amino acidsubstitution comprises E233P/L234V/L235A/G236+A327G/A330S/P331S.
 6. Theantibody of claim 1, comprising the variable region sequences of SEQ IDNO:1 and SEQ ID NO:2; or SEQ ID NO:9 and SEQ ID NO:10.
 7. Apharmaceutical composition comprising an antibody set forth in claim 1.8. The composition of claim 7, in a unit dose formulation.
 9. Thecomposition of claim 8, provided as a sterile pre-pack in a unit dosewith diluent.
 10. The composition of claim 7, further comprising asecond therapeutic antibody.
 11. A method of increasing phagocytosis ofa targeted cell in a human subject, the method comprising: administeringto the subject a composition comprising an antibody set forth in claim1, in a dose effective to increase phagocytosis of the targeted cell.12. The method according to claim 11, wherein the targeted cell is acancer cell.
 13. The method according to claim 11, further comprisingadministering a second therapeutic antibody.
 14. The method of claim 13,wherein the second therapeutic antibody binds to a protein on thesurface of a cancer cell.